7KPC | pdb_00007kpc

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88Q mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site

PDB DOI: https://doi.org/10.2210/pdb7KPC/pdb

Classification: LYASE
Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-11-10 Released: 2021-11-17
Deposition Author(s): Saran, S., Sanders, D.A.R.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.169 (Depositor), 0.170 (DCC)
R-Value Work:
0.142 (Depositor), 0.150 (DCC)
R-Value Observed:
0.143 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

THE ALLOSTERIC SITE RESIDUE, E88 INTERACTS WITH THE INHIBITORS TO TRANSMIT THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS BY FORMING A HYDROGEN BOND.

Saran, S., Majdi Yazdi, M., Chung, I., Sanders, D.A.R.

To be published.

Macromolecule Content

Total Structure Weight: 212 kDa
Atom Count: 15,646
Modeled Residue Count: 1,777
Deposited Residue Count: 1,860
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate synthase	A, B, C, D, E A, B, C, D, E, F	310	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 1 Gene Names: dapA, Cj0806 EC: 4.3.3.7
UniProt
Find proteins for Q9PPB4 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q9PPB4 Go to UniProtKB: Q9PPB4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9PPB4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE (Subject of Investigation/LOI) Query on PGE Download Ideal Coordinates CCD File SDF format, chain BC [auth E] SDF format, chain OB [auth D] SDF format, chain TA [auth C] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain SA [auth C] SDF format, chain NB [auth D] SDF format, chain MB [auth D] SDF format, chain LC [auth F] SDF format, chain GA [auth B] MOL2 format, chain BC [auth E] MOL2 format, chain OB [auth D] MOL2 format, chain TA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain NB [auth D] MOL2 format, chain MB [auth D] MOL2 format, chain LC [auth F] MOL2 format, chain GA [auth B] mmCIF format, chain BC [auth E] mmCIF format, chain OB [auth D] mmCIF format, chain TA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain NB [auth D] mmCIF format, chain MB [auth D] mmCIF format, chain LC [auth F] mmCIF format, chain GA [auth B]	BC [auth E] GA [auth B] LC [auth F] MB [auth D] NB [auth D] BC [auth E], GA [auth B], LC [auth F], MB [auth D], NB [auth D], OB [auth D], SA [auth C], TA [auth C], U [auth A], V [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain BC [auth E] Focus chain GA [auth B] Focus chain LC [auth F] Focus chain MB [auth D] Focus chain NB [auth D] Focus chain OB [auth D] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain BC [auth E] Focus chain GA [auth B] Focus chain LC [auth F] Focus chain MB [auth D] Focus chain NB [auth D] Focus chain OB [auth D] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain U [auth A] Focus chain V [auth A]
LYS (Subject of Investigation/LOI) Query on LYS Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain CC [auth F] SDF format, chain G [auth A] SDF format, chain JA [auth C] SDF format, chain RB [auth E] SDF format, chain X [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain CC [auth F] MOL2 format, chain G [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain RB [auth E] MOL2 format, chain X [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain CC [auth F] mmCIF format, chain G [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain RB [auth E] mmCIF format, chain X [auth B]	AB [auth D] CC [auth F] G [auth A] JA [auth C] RB [auth E] AB [auth D], CC [auth F], G [auth A], JA [auth C], RB [auth E], X [auth B]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain AB [auth D] Focus chain CC [auth F] Focus chain G [auth A] Focus chain JA [auth C] Focus chain RB [auth E] Focus chain X [auth B] Interactions & Density Focus chain AB [auth D] Focus chain CC [auth F] Focus chain G [auth A] Focus chain JA [auth C] Focus chain RB [auth E] Focus chain X [auth B]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain MC [auth F] SDF format, chain OC [auth F] SDF format, chain VA [auth C] SDF format, chain W [auth A] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain ZA [auth C] SDF format, chain YA [auth C] SDF format, chain UA [auth C] SDF format, chain PB [auth D] SDF format, chain NC [auth F] MOL2 format, chain HA [auth B] MOL2 format, chain MC [auth F] MOL2 format, chain OC [auth F] MOL2 format, chain VA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain PB [auth D] MOL2 format, chain NC [auth F] mmCIF format, chain HA [auth B] mmCIF format, chain MC [auth F] mmCIF format, chain OC [auth F] mmCIF format, chain VA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain PB [auth D] mmCIF format, chain NC [auth F]	HA [auth B] MC [auth F] NC [auth F] OC [auth F] PB [auth D] HA [auth B], MC [auth F], NC [auth F], OC [auth F], PB [auth D], UA [auth C], VA [auth C], W [auth A], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain MC [auth F] Focus chain NC [auth F] Focus chain OC [auth F] Focus chain PB [auth D] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain HA [auth B] Focus chain MC [auth F] Focus chain NC [auth F] Focus chain OC [auth F] Focus chain PB [auth D] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain QB [auth D] SDF format, chain PC [auth F] SDF format, chain IA [auth B] MOL2 format, chain QB [auth D] MOL2 format, chain PC [auth F] MOL2 format, chain IA [auth B] mmCIF format, chain QB [auth D] mmCIF format, chain PC [auth F] mmCIF format, chain IA [auth B]	IA [auth B], PC [auth F], QB [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain IA [auth B] Focus chain PC [auth F] Focus chain QB [auth D] Interactions & Density Focus chain IA [auth B] Focus chain PC [auth F] Focus chain QB [auth D]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain FB [auth D] SDF format, chain GB [auth D] SDF format, chain GC [auth F] SDF format, chain HC [auth F] SDF format, chain IC [auth F] SDF format, chain JB [auth D] SDF format, chain JC [auth F] SDF format, chain KB [auth D] SDF format, chain KC [auth F] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain ZB [auth E] SDF format, chain YB [auth E] SDF format, chain XB [auth E] SDF format, chain RA [auth C] SDF format, chain QA [auth C] SDF format, chain PA [auth C] SDF format, chain OA [auth C] SDF format, chain LB [auth D] SDF format, chain IB [auth D] SDF format, chain HB [auth D] SDF format, chain FA [auth B] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain AC [auth E] MOL2 format, chain CA [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain GB [auth D] MOL2 format, chain GC [auth F] MOL2 format, chain HC [auth F] MOL2 format, chain IC [auth F] MOL2 format, chain JB [auth D] MOL2 format, chain JC [auth F] MOL2 format, chain KB [auth D] MOL2 format, chain KC [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain ZB [auth E] MOL2 format, chain YB [auth E] MOL2 format, chain XB [auth E] MOL2 format, chain RA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain LB [auth D] MOL2 format, chain IB [auth D] MOL2 format, chain HB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain AC [auth E] mmCIF format, chain CA [auth B] mmCIF format, chain FB [auth D] mmCIF format, chain GB [auth D] mmCIF format, chain GC [auth F] mmCIF format, chain HC [auth F] mmCIF format, chain IC [auth F] mmCIF format, chain JB [auth D] mmCIF format, chain JC [auth F] mmCIF format, chain KB [auth D] mmCIF format, chain KC [auth F] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain ZB [auth E] mmCIF format, chain YB [auth E] mmCIF format, chain XB [auth E] mmCIF format, chain RA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain LB [auth D] mmCIF format, chain IB [auth D] mmCIF format, chain HB [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain AC [auth E]	AC [auth E] CA [auth B] DA [auth B] EA [auth B] FA [auth B] AC [auth E], CA [auth B], DA [auth B], EA [auth B], FA [auth B], FB [auth D], GB [auth D], GC [auth F], HB [auth D], HC [auth F], IB [auth D], IC [auth F], JB [auth D], JC [auth F], KB [auth D], KC [auth F], LB [auth D], OA [auth C], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], T [auth A], XB [auth E], YB [auth E], ZB [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AC [auth E] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain GC [auth F] Focus chain HB [auth D] Focus chain HC [auth F] Focus chain IB [auth D] Focus chain IC [auth F] Focus chain JB [auth D] Focus chain JC [auth F] Focus chain KB [auth D] Focus chain KC [auth F] Focus chain LB [auth D] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain T [auth A] Focus chain XB [auth E] Focus chain YB [auth E] Focus chain ZB [auth E] Interactions & Density Focus chain AC [auth E] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain GC [auth F] Focus chain HB [auth D] Focus chain HC [auth F] Focus chain IB [auth D] Focus chain IC [auth F] Focus chain JB [auth D] Focus chain JC [auth F] Focus chain KB [auth D] Focus chain KC [auth F] Focus chain LB [auth D] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain T [auth A] Focus chain XB [auth E] Focus chain YB [auth E] Focus chain ZB [auth E]
ACT (Subject of Investigation/LOI) Query on ACT Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CB [auth D] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain VB [auth E] SDF format, chain WB [auth E] SDF format, chain UB [auth E] SDF format, chain P [auth A] SDF format, chain NA [auth C] SDF format, chain LA [auth C] SDF format, chain FC [auth F] SDF format, chain EC [auth F] SDF format, chain EB [auth D] SDF format, chain DB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain VB [auth E] MOL2 format, chain WB [auth E] MOL2 format, chain UB [auth E] MOL2 format, chain P [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain FC [auth F] MOL2 format, chain EC [auth F] MOL2 format, chain EB [auth D] MOL2 format, chain DB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain MA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain VB [auth E] mmCIF format, chain WB [auth E] mmCIF format, chain UB [auth E] mmCIF format, chain P [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain FC [auth F] mmCIF format, chain EC [auth F] mmCIF format, chain EB [auth D] mmCIF format, chain DB [auth D]	BA [auth B] CB [auth D] DB [auth D] EB [auth D] EC [auth F] BA [auth B], CB [auth D], DB [auth D], EB [auth D], EC [auth F], FC [auth F], LA [auth C], MA [auth C], N [auth A], NA [auth C], O [auth A], P [auth A], UB [auth E], VB [auth E], WB [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BA [auth B] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain EC [auth F] Focus chain FC [auth F] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain UB [auth E] Focus chain VB [auth E] Focus chain WB [auth E] Interactions & Density Focus chain BA [auth B] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain EC [auth F] Focus chain FC [auth F] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain UB [auth E] Focus chain VB [auth E] Focus chain WB [auth E]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain BB [auth D] SDF format, chain DC [auth F] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain M [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain TB [auth E] SDF format, chain SB [auth E] SDF format, chain L [auth A] SDF format, chain I [auth A] SDF format, chain AA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain DC [auth F] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain TB [auth E] MOL2 format, chain SB [auth E] MOL2 format, chain L [auth A] MOL2 format, chain I [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain BB [auth D] mmCIF format, chain DC [auth F] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain TB [auth E] mmCIF format, chain SB [auth E] mmCIF format, chain L [auth A] mmCIF format, chain I [auth A] mmCIF format, chain AA [auth B]	AA [auth B] BB [auth D] DC [auth F] H [auth A] I [auth A] AA [auth B], BB [auth D], DC [auth F], H [auth A], I [auth A], J [auth A], K [auth A], KA [auth C], L [auth A], M [auth A], SB [auth E], TB [auth E], Y [auth B], Z [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BB [auth D] Focus chain DC [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain SB [auth E] Focus chain TB [auth E] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BB [auth D] Focus chain DC [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain SB [auth E] Focus chain TB [auth E] Focus chain Y [auth B] Focus chain Z [auth B]