Research workbench

[fefe]-hydrogenase cpi from clostridium pasteurianum, variant E282A

Analyse [fefe]-hydrogenase cpi from clostridium pasteurianum, variant E282A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GM1
Type: protein
Length: 1,150 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Iron hydrogenase 1
EC: 1.12.7.2
UniProt: P29166
Ligands: SF4, 402, FES, MG
Pockets: 18 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Iron hydrogenase 1 (EC 1.12.7.2)	protein	575	43% helix, 16% strand	P29166

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 8 copies · chains A, B
402 · dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) · ligand · 2 copies · chains A, B
FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 3 copies · chains A, B

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

Pockets

18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	110	0.81	0.99	29	402, SF4
2	110	0.80	0.99	33	402, SF4
3	326	0.71	0.84	41	empty
4	358	0.70	0.83	54	empty
5	449	0.69	0.81	55	MG

Interfaces

1 interface between chains.

A–B · 1542 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6GM1 · [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282A · the same entry in another collection · chain A against A, TM-score 1.00
P29166 · AlphaFold monomer V2.0 prediction for iron hydrogenase 1 (P29166) · a predicted model of the same protein · chain A 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 P29166
Elsewhere: RCSB PDB 6GM1 · PDBe 6GM1 · UniProt P29166

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