MolNFT v1 · #26465 · protein

Crystal structure of ipmdh from sulfolobus tokodaii

1WPW · 3-isopropylmalate dehydrogenase: “Crystal structure of ipmdh from sulfolobus tokodaii”. X-ray diffraction, 1 ligand (MG), 7 pockets (best druggability 0.74). MolNFT v1 #26465 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1WPW
Type: protein
Length: 672 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-isopropylmalate dehydrogenase
EC: 1.1.1.85
UniProt: P50455
Ligands: MG
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	3-isopropylmalate dehydrogenase (EC 1.1.1.85)	protein	336	45% helix, 21% strand	P50455

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	236	0.74	0.89	35	empty
2	223	0.74	0.89	36	empty
3	472	0.64	0.78	40	MG
4	464	0.64	0.78	37	MG
5	55	0.35	0.78	11	empty

Interfaces

1 interface between chains.

A–B · 1852 Å² buried · 26 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

1WPW · Crystal Structure of IPMDH from Sulfolobus tokodaii · the same entry in another collection · chain B against B, TM-score 1.00
P50455 · AlphaFold monomer V2.0 prediction for 3-isopropylmalate dehydrogenase (P50455) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P50455
Elsewhere: RCSB PDB 1WPW · PDBe 1WPW · UniProt P50455

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