MolNFT v1 · #141755 · protein

MDH3 wild type, NAD-form

5ZI2 · Malate dehydrogenase: “MDH3 wild type, NAD-form”. X-ray diffraction, 3 ligands (NAD, ADP, CL), 5 pockets (best druggability 0.74). MolNFT v1 #141755 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZI2
Type: protein
Length: 678 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: NAD, ADP, CL
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 54% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Malate dehydrogenase (EC 1.1.1.37)	protein	339	54% helix, 17% strand	A0A250W9L1

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
ADP · Adenosine-5'-diphosphate · ligand · chains B
CL · Chloride ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · chains A

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	421	0.74	0.84	57	NAD
2	515	0.72	0.81	57	ADP
3	439	0.68	0.79	44	empty
4	80	0.38	0.77	14	empty
5	51	0.25	0.73	19	empty

Interfaces

1 interface between chains.

A–B · 1659 Å² buried · 36 hydrogen bonds · protein-protein

Compared structures

5ZI2 · MDH3 wild type, nad-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 5ZI2 · PDBe 5ZI2 · UniProt A0A250W9L1

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