6M3S | pdb_00006m3s

Dimeric isocitrate dehydrogenase from Xanthomonas campestris pv. campestris 8004

PDB DOI: https://doi.org/10.2210/pdb6M3S/pdb

Classification: OXIDOREDUCTASE
Organism(s): Xanthomonas campestris
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-03-04 Released: 2021-03-10
Deposition Author(s): Zhu, G.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.225 (Depositor), 0.220 (DCC)
R-Value Work:
0.175 (Depositor), 0.170 (DCC)
R-Value Observed:
0.177 (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

Dimeric isocitrate dehydrogenase from Xanthomonas campestris pv. campestris 8004

Zhu, G.P.

To be published.

Macromolecule Content

Total Structure Weight: 75.13 kDa
Atom Count: 5,393
Modeled Residue Count: 671
Deposited Residue Count: 686
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 dehydrogenase	A, B	343	Xanthomonas campestris	Mutation(s): 0 Gene Names: D0A35_19175, TR80_00940, XcmpCFBP7700_13825 EC: 1.1.1.41
UniProt
Find proteins for A0A0H2XBX7 (Xanthomonas campestris pv. campestris (strain 8004)) Explore A0A0H2XBX7 Go to UniProtKB: A0A0H2XBX7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2XBX7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
ICA Query on ICA Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	ISOCITRATE CALCIUM COMPLEX C₆ H₇ Ca O₇ AHEGTOWQUJMCIO-YCWPWOODSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]