6LRT | pdb_00006lrt

Crystal structure of isocitrate lyase (Caur_3889) from Chloroflexus aurantiacus in complex with isocitrate and manganese ion

PDB DOI: https://doi.org/10.2210/pdb6LRT/pdb

Classification: LYASE
Organism(s): Chloroflexus aurantiacus J-10-fl
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-01-16 Released: 2021-07-28
Deposition Author(s): Lee, S.H., Kim, K.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.246 (Depositor), 0.250 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural studies reveal the molecular mechanism of isocitrate lyase from Chloroflexus aurantiacus

Lee, S.H., Kim, K.J.

To be published.

Macromolecule Content

Total Structure Weight: 389.37 kDa
Atom Count: 27,179
Modeled Residue Count: 3,384
Deposited Residue Count: 3,488
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate lyase	A B [auth D] C [auth G] D [auth J] E [auth M] A, B [auth D], C [auth G], D [auth J], E [auth M], F [auth P], G [auth S], H [auth V]	436	Chloroflexus aurantiacus J-10-fl	Mutation(s): 0 Gene Names: Caur_3889 EC: 4.1.3.1
UniProt
Find proteins for A9WDE7 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)) Explore A9WDE7 Go to UniProtKB: A9WDE7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9WDE7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ICT (Subject of Investigation/LOI) Query on ICT Download Ideal Coordinates CCD File SDF format, chain BA [auth S] SDF format, chain GA [auth V] SDF format, chain I [auth A] SDF format, chain L [auth D] SDF format, chain O [auth G] SDF format, chain S [auth J] SDF format, chain W [auth M] SDF format, chain Y [auth P] MOL2 format, chain BA [auth S] MOL2 format, chain GA [auth V] MOL2 format, chain I [auth A] MOL2 format, chain L [auth D] MOL2 format, chain O [auth G] MOL2 format, chain S [auth J] MOL2 format, chain W [auth M] MOL2 format, chain Y [auth P] mmCIF format, chain BA [auth S] mmCIF format, chain GA [auth V] mmCIF format, chain I [auth A] mmCIF format, chain L [auth D] mmCIF format, chain O [auth G] mmCIF format, chain S [auth J] mmCIF format, chain W [auth M] mmCIF format, chain Y [auth P]	BA [auth S] GA [auth V] I [auth A] L [auth D] O [auth G] BA [auth S], GA [auth V], I [auth A], L [auth D], O [auth G], S [auth J], W [auth M], Y [auth P]	ISOCITRIC ACID C₆ H₈ O₇ ODBLHEXUDAPZAU-ZAFYKAAXSA-N		Interactions Focus chain BA [auth S] Focus chain GA [auth V] Focus chain I [auth A] Focus chain L [auth D] Focus chain O [auth G] Focus chain S [auth J] Focus chain W [auth M] Focus chain Y [auth P] Interactions & Density Focus chain BA [auth S] Focus chain GA [auth V] Focus chain I [auth A] Focus chain L [auth D] Focus chain O [auth G] Focus chain S [auth J] Focus chain W [auth M] Focus chain Y [auth P]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth S] SDF format, chain DA [auth S] SDF format, chain EA [auth S] SDF format, chain HA [auth V] SDF format, chain IA [auth V] SDF format, chain J [auth A] SDF format, chain M [auth D] SDF format, chain P [auth G] SDF format, chain Q [auth G] SDF format, chain T [auth J] SDF format, chain U [auth J] SDF format, chain Z [auth P] MOL2 format, chain CA [auth S] MOL2 format, chain DA [auth S] MOL2 format, chain EA [auth S] MOL2 format, chain HA [auth V] MOL2 format, chain IA [auth V] MOL2 format, chain J [auth A] MOL2 format, chain M [auth D] MOL2 format, chain P [auth G] MOL2 format, chain Q [auth G] MOL2 format, chain T [auth J] MOL2 format, chain U [auth J] MOL2 format, chain Z [auth P] mmCIF format, chain CA [auth S] mmCIF format, chain DA [auth S] mmCIF format, chain EA [auth S] mmCIF format, chain HA [auth V] mmCIF format, chain IA [auth V] mmCIF format, chain J [auth A] mmCIF format, chain M [auth D] mmCIF format, chain P [auth G] mmCIF format, chain Q [auth G] mmCIF format, chain T [auth J] mmCIF format, chain U [auth J] mmCIF format, chain Z [auth P]	CA [auth S] DA [auth S] EA [auth S] HA [auth V] IA [auth V] CA [auth S], DA [auth S], EA [auth S], HA [auth V], IA [auth V], J [auth A], M [auth D], P [auth G], Q [auth G], T [auth J], U [auth J], Z [auth P]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth S] Focus chain DA [auth S] Focus chain EA [auth S] Focus chain HA [auth V] Focus chain IA [auth V] Focus chain J [auth A] Focus chain M [auth D] Focus chain P [auth G] Focus chain Q [auth G] Focus chain T [auth J] Focus chain U [auth J] Focus chain Z [auth P] Interactions & Density Focus chain CA [auth S] Focus chain DA [auth S] Focus chain EA [auth S] Focus chain HA [auth V] Focus chain IA [auth V] Focus chain J [auth A] Focus chain M [auth D] Focus chain P [auth G] Focus chain Q [auth G] Focus chain T [auth J] Focus chain U [auth J] Focus chain Z [auth P]
MN (Subject of Investigation/LOI) Query on MN Download Ideal Coordinates CCD File SDF format, chain AA [auth P] SDF format, chain FA [auth S] SDF format, chain JA [auth V] SDF format, chain K [auth A] SDF format, chain N [auth D] SDF format, chain R [auth G] SDF format, chain V [auth J] SDF format, chain X [auth M] MOL2 format, chain AA [auth P] MOL2 format, chain FA [auth S] MOL2 format, chain JA [auth V] MOL2 format, chain K [auth A] MOL2 format, chain N [auth D] MOL2 format, chain R [auth G] MOL2 format, chain V [auth J] MOL2 format, chain X [auth M] mmCIF format, chain AA [auth P] mmCIF format, chain FA [auth S] mmCIF format, chain JA [auth V] mmCIF format, chain K [auth A] mmCIF format, chain N [auth D] mmCIF format, chain R [auth G] mmCIF format, chain V [auth J] mmCIF format, chain X [auth M]	AA [auth P] FA [auth S] JA [auth V] K [auth A] N [auth D] AA [auth P], FA [auth S], JA [auth V], K [auth A], N [auth D], R [auth G], V [auth J], X [auth M]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth P] Focus chain FA [auth S] Focus chain JA [auth V] Focus chain K [auth A] Focus chain N [auth D] Focus chain R [auth G] Focus chain V [auth J] Focus chain X [auth M] Interactions & Density Focus chain AA [auth P] Focus chain FA [auth S] Focus chain JA [auth V] Focus chain K [auth A] Focus chain N [auth D] Focus chain R [auth G] Focus chain V [auth J] Focus chain X [auth M]