MolNFT v1 · #186688 · protein

Human malate dehydrogenase I (mdhi)

7RM9 · Malate dehydrogenase, cytoplasmic: “Human malate dehydrogenase I (mdhi)”. X-ray diffraction, 5 pockets (best druggability 0.67). MolNFT v1 #186688 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7RM9
Type: protein
Length: 658 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Malate dehydrogenase, cytoplasmic
EC: 1.1.1.37, 1.1.1.96
UniProt: P40925
Pockets: 5 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Malate dehydrogenase, cytoplasmic (EC 1.1.1.37, 1.1.1.96)	protein	333	46% helix, 20% strand	P40925
B	Malate dehydrogenase, cytoplasmic (EC 1.1.1.37, 1.1.1.96)	protein	325	45% helix, 20% strand	P40925

Ligands and binding sites

MLI · Malonate ion · 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	294	0.67	0.82	39	MLI
2	390	0.59	0.76	50	empty
3	121	0.52	0.81	15	empty
4	285	0.51	0.74	44	empty
5	163	0.51	0.78	21	empty

Interfaces

1 interface between chains.

A–B · 1796 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

7RM9 · Human Malate Dehydrogenase I (MDHI) · the same entry in another collection · chain A against A, TM-score 1.00
P40925 · AlphaFold monomer V2.0 prediction for malate dehydrogenase, cytoplasmic (P40925) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P40925
Elsewhere: RCSB PDB 7RM9 · PDBe 7RM9 · UniProt P40925

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