5KVU

Crystal structure of isocitrate dehydrogenase-2 in complex with NADP(+) from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb5KVU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-07-15 Released: 2017-07-19
Deposition Author(s): Cheng, Y.S., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.66 Å
R-Value Free: 0.228
R-Value Work: 0.178
R-Value Observed: 0.181

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 and kinetic characterization of isocitrate dehydrogenase-2 from Mycobacterium tuberculosis

Sacchettini, J.C., Cheng, Y.S.

To be published.

Macromolecule Content

Total Structure Weight: 334.59 kDa
Atom Count: 23,607
Modelled Residue Count: 2,942
Deposited Residue Count: 2,980
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, C, D	745	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: icd2, Rv0066c, LH57_00380 EC: 1.1.1.42
UniProt
Find proteins for O53611 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O53611 Go to UniProtKB: O53611
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O53611
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth D]	E [auth A], H [auth B], L [auth C], Q [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain Q [auth D]
MLT Query on MLT Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SIN Query on SIN Download Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C]	M [auth C]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
MLA Query on MLA Download Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain I [auth B] MOL2 format, chain R [auth D] MOL2 format, chain I [auth B]	I [auth B], R [auth D]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain R [auth D] Interactions & Density Focus chain I [auth B] Focus chain R [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain S [auth D] MOL2 format, chain N [auth C] MOL2 format, chain S [auth D]	N [auth C], S [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain N [auth C] Focus chain S [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D]	G [auth A] J [auth B] K [auth B] O [auth C] P [auth C] G [auth A], J [auth B], K [auth B], O [auth C], P [auth C], T [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D]