MolNFT v1 · #141757 · protein

MDH3 wild type, NAD-oaa-form

5ZI4 · Malate dehydrogenase: “MDH3 wild type, NAD-oaa-form”. X-ray diffraction, 2 ligands (OAA, NAD), 4 pockets (best druggability 0.81). MolNFT v1 #141757 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZI4
Type: protein
Length: 677 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Malate dehydrogenase
EC: 1.1.1.37
UniProt: A0A250W9L1
Ligands: OAA, NAD
Pockets: 4 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Malate dehydrogenase (EC 1.1.1.37)	protein	339	50% helix, 17% strand	A0A250W9L1
B	Malate dehydrogenase (EC 1.1.1.37)	protein	338	51% helix, 17% strand	A0A250W9L1

Ligands and binding sites

OAA · Oxaloacetate ion · ligand · 2 copies · chains A, B
NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1085	0.81	0.83	137	OAA, NAD
2	325	0.59	0.77	33	empty
3	50	0.30	0.77	15	empty
4	63	0.28	0.74	22	empty

Interfaces

1 interface between chains.

A–B · 1677 Å² buried · 35 hydrogen bonds · protein-protein

Compared structures

5ZI4 · MDH3 wild type, nad-oaa-form · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A0A250W9L1
Elsewhere: RCSB PDB 5ZI4 · PDBe 5ZI4 · UniProt A0A250W9L1

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