7KNZ | pdb_00007knz

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88A mutant with pyruvate bound in the active site and R,R-bislysine at the allosteric site

PDB DOI: https://doi.org/10.2210/pdb7KNZ/pdb

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

Deposited: 2020-11-06 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: 2.28 Å
R-Value Free:
0.216 (Depositor), 0.220 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
View more details

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: 209.78 kDa
Atom Count: 14,744
Modeled Residue Count: 1,776
Deposited Residue Count: 1,860
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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
3VN (Subject of Investigation/LOI) Query on 3VN Download Ideal Coordinates CCD File SDF format, chain IB [auth F] SDF format, chain OA [auth D] SDF format, chain T [auth B] MOL2 format, chain IB [auth F] MOL2 format, chain OA [auth D] MOL2 format, chain T [auth B] mmCIF format, chain IB [auth F] mmCIF format, chain OA [auth D] mmCIF format, chain T [auth B]	IB [auth F], OA [auth D], T [auth B]	(2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid C₁₄ H₃₀ N₄ O₄ XYUHPPVEDOOPDE-ZIAGYGMSSA-N		Interactions Focus chain IB [auth F] Focus chain OA [auth D] Focus chain T [auth B] Interactions & Density Focus chain IB [auth F] Focus chain OA [auth D] Focus chain T [auth B]
PGE (Subject of Investigation/LOI) Query on PGE Download Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain M [auth A] SDF format, chain SA [auth D] SDF format, chain Z [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain Z [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain SA [auth D] mmCIF format, chain Z [auth B]	IA [auth C], M [auth A], SA [auth D], Z [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Focus chain M [auth A] Focus chain SA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain IA [auth C] Focus chain M [auth A] Focus chain SA [auth D] Focus chain Z [auth B]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain DB [auth E] SDF format, chain EB [auth E] SDF format, chain L [auth A] SDF format, chain LB [auth F] SDF format, chain MB [auth F] SDF format, chain NB [auth F] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain FB [auth E] MOL2 format, chain DB [auth E] MOL2 format, chain EB [auth E] MOL2 format, chain L [auth A] MOL2 format, chain LB [auth F] MOL2 format, chain MB [auth F] MOL2 format, chain NB [auth F] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain FB [auth E] mmCIF format, chain DB [auth E] mmCIF format, chain EB [auth E] mmCIF format, chain L [auth A] mmCIF format, chain LB [auth F] mmCIF format, chain MB [auth F] mmCIF format, chain NB [auth F] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain FB [auth E]	DB [auth E] EB [auth E] FB [auth E] L [auth A] LB [auth F] DB [auth E], EB [auth E], FB [auth E], L [auth A], LB [auth F], MB [auth F], NB [auth F], X [auth B], Y [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain DB [auth E] Focus chain EB [auth E] Focus chain FB [auth E] Focus chain L [auth A] Focus chain LB [auth F] Focus chain MB [auth F] Focus chain NB [auth F] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain DB [auth E] Focus chain EB [auth E] Focus chain FB [auth E] Focus chain L [auth A] Focus chain LB [auth F] Focus chain MB [auth F] Focus chain NB [auth F] Focus chain X [auth B] Focus chain Y [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain NA [auth C] SDF format, chain PB [auth F] MOL2 format, chain NA [auth C] MOL2 format, chain PB [auth F] mmCIF format, chain NA [auth C] mmCIF format, chain PB [auth F]	NA [auth C], PB [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain NA [auth C] Focus chain PB [auth F] Interactions & Density Focus chain NA [auth C] Focus chain PB [auth F]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain HB [auth E] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OB [auth F] SDF format, chain P [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain TA [auth D] SDF format, chain UA [auth D] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain XA [auth D] SDF format, chain YA [auth D] SDF format, chain Q [auth A] SDF format, chain GB [auth E] SDF format, chain DA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain HB [auth E] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth F] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain XA [auth D] MOL2 format, chain YA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain GB [auth E] MOL2 format, chain DA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain HB [auth E] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OB [auth F] mmCIF format, chain P [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain TA [auth D] mmCIF format, chain UA [auth D] mmCIF format, chain VA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain XA [auth D] mmCIF format, chain YA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain GB [auth E] mmCIF format, chain DA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] GB [auth E] AA [auth B], BA [auth B], CA [auth B], DA [auth B], GB [auth E], HB [auth E], JA [auth C], KA [auth C], LA [auth C], MA [auth C], N [auth A], O [auth A], OB [auth F], P [auth A], Q [auth A], R [auth A], S [auth A], TA [auth D], UA [auth D], VA [auth D], WA [auth D], XA [auth D], YA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain GB [auth E] Focus chain HB [auth E] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain OB [auth F] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain YA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain GB [auth E] Focus chain HB [auth E] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain OB [auth F] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain YA [auth D]
ACT (Subject of Investigation/LOI) Query on ACT Download Ideal Coordinates CCD File SDF format, chain BB [auth E] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KB [auth F] SDF format, chain W [auth B] SDF format, chain RA [auth D] SDF format, chain JB [auth F] SDF format, chain I [auth A] SDF format, chain CB [auth E] MOL2 format, chain BB [auth E] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth F] MOL2 format, chain W [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain JB [auth F] MOL2 format, chain I [auth A] MOL2 format, chain CB [auth E] mmCIF format, chain BB [auth E] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KB [auth F] mmCIF format, chain W [auth B] mmCIF format, chain RA [auth D] mmCIF format, chain JB [auth F] mmCIF format, chain I [auth A] mmCIF format, chain CB [auth E]	BB [auth E] CB [auth E] GA [auth C] HA [auth C] I [auth A] BB [auth E], CB [auth E], GA [auth C], HA [auth C], I [auth A], J [auth A], JB [auth F], K [auth A], KB [auth F], RA [auth D], W [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BB [auth E] Focus chain CB [auth E] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain JB [auth F] Focus chain K [auth A] Focus chain KB [auth F] Focus chain RA [auth D] Focus chain W [auth B] Interactions & Density Focus chain BB [auth E] Focus chain CB [auth E] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain JB [auth F] Focus chain K [auth A] Focus chain KB [auth F] Focus chain RA [auth D] Focus chain W [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain ZA [auth E] SDF format, chain QA [auth D] SDF format, chain PA [auth D] SDF format, chain EA [auth C] MOL2 format, chain AB [auth E] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain ZA [auth E] MOL2 format, chain QA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain EA [auth C] mmCIF format, chain AB [auth E] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain ZA [auth E] mmCIF format, chain QA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain EA [auth C]	AB [auth E] EA [auth C] FA [auth C] G [auth A] H [auth A] AB [auth E], EA [auth C], FA [auth C], G [auth A], H [auth A], PA [auth D], QA [auth D], U [auth B], V [auth B], ZA [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain ZA [auth E] Interactions & Density Focus chain AB [auth E] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain ZA [auth E]