4WLF

Crystal structure of L-malate bound MDH2

PDB DOI: https://doi.org/10.2210/pdb4WLF/pdb

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

Deposited: 2014-10-07 Released: 2015-11-25
Deposition Author(s): Eo, Y.M., Han, B.G., Ahn, H.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.247
R-Value Work: 0.227
R-Value Observed: 0.228

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of L-malate bound MDH2

Eo, Y.M., Han, B.G., Ahn, H.C.

To be published.

Macromolecule Content

Total Structure Weight: 144.34 kDa
Atom Count: 9,351
Modelled Residue Count: 1,256
Deposited Residue Count: 1,360
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase, mitochondrial	A, B, C, D	340	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40926
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMR Query on LMR Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain E [auth A] SDF format, chain K [auth D] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	(2S)-2-hydroxybutanedioic acid C₄ H₆ O₅ BJEPYKJPYRNKOW-REOHCLBHSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.247
R-Value Work: 0.227
R-Value Observed: 0.228
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.246	α = 90
b = 152.183	β = 90
c = 155.034	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-11-25

Deposition Author(s):

Eo, Y.M.

Han, B.G.

Ahn, H.C.

Revision History (Full details and data files)

Version 1.0: 2015-11-25
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

4WLF

Crystal structure of L-malate bound MDH2

Crystal structure of L-malate bound MDH2

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)