4WLV

Crystal structure of NAD bound MDH2

PDB DOI: https://doi.org/10.2210/pdb4WLV/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: 2.40 Å
R-Value Free: 0.248
R-Value Work: 0.209
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of NAD bound MDH2

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

To be published.

Macromolecule Content

Total Structure Weight: 146.84 kDa
Atom Count: 9,514
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
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D]	E [auth A], H [auth B], K [auth C], N [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D]	F [auth A] G [auth A] I [auth B] J [auth B] L [auth C] F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D]