4WLU | pdb_00004wlu

Crystal structure of L-malate and NAD bound MDH2

PDB DOI: https://doi.org/10.2210/pdb4WLU/pdb

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

Deposited: 2014-10-08 Released: 2015-11-25
Deposition Author(s): Eo, Y.M., Han, B.G., Ahn, H.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.244 (Depositor), 0.248 (DCC)
R-Value Work:
0.216 (Depositor), 0.222 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of L-malate and NAD bound MDH2

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

To be published.

Macromolecule Content

Total Structure Weight: 146.61 kDa
Atom Count: 9,562
Modeled Residue Count: 1,256
Deposited Residue Count: 1,360
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40926
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		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]
LMR Query on LMR Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.244 (Depositor), 0.248 (DCC)
R-Value Work: 0.216 (Depositor), 0.222 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.982	α = 90
b = 152.14	β = 90
c = 155.035	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):

Revision History (Full details and data files)

Version 1.0: 2015-11-25
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.