2DFD | pdb_00002dfd

Crystal Structure of Human Malate Dehydrogenase Type 2

PDB DOI: https://doi.org/10.2210/pdb2DFD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-02-28 Released: 2006-03-28
Deposition Author(s): Ugochukwu, E., Shafqat, N., Rojkova, A., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A., von Delft, F., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.194 (Depositor), 0.200 (DCC)
R-Value Work:
0.156 (Depositor), 0.163 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Crystal Structure of Human Malate Dehydrogenase Type 2

Ugochukwu, E., Shafqat, N., Rojkova, A., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A., von Delft, F., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 148.97 kDa
Atom Count: 10,300
Modeled Residue Count: 1,256
Deposited Residue Count: 1,368
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B, C, D	342	Homo sapiens	Mutation(s): 0 Gene Names: MDH2 EC: 1.1.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for P40926 (Homo sapiens) Explore P40926 Go to UniProtKB: P40926
PHAROS: P40926 GTEx: ENSG00000146701
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40926
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain R [auth C] SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain W [auth D] MOL2 format, chain R [auth C] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain W [auth D] mmCIF format, chain R [auth C] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	H [auth A], M [auth B], R [auth C], W [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth D]
HIS Query on HIS Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain N [auth B] SDF format, chain I [auth A] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] mmCIF format, chain S [auth C] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A]	I [auth A], N [auth B], S [auth C]	HISTIDINE C₆ H₁₀ N₃ O₂ HNDVDQJCIGZPNO-YFKPBYRVSA-O		Interactions Focus chain I [auth A] Focus chain N [auth B] Focus chain S [auth C] Interactions & Density Focus chain I [auth A] Focus chain N [auth B] Focus chain S [auth C]
LMR Query on LMR Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B], O [auth C], T [auth D]	(2S)-2-hydroxybutanedioic acid C₄ H₆ O₅ BJEPYKJPYRNKOW-REOHCLBHSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D]
ALA Query on ALA Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] L [auth B] P [auth C] Q [auth C] F [auth A], G [auth A], L [auth B], P [auth C], Q [auth C], U [auth D], V [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.194 (Depositor), 0.200 (DCC)
R-Value Work: 0.156 (Depositor), 0.163 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.943	α = 90
b = 152.526	β = 90
c = 154.827	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-03-28

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2006-03-28
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2025-10-29
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary