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1.39 ångström crystal structure of fe-only hydrogenase

Analyse 1.39 ångström crystal structure of fe-only hydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3C8Y
Type: protein
Length: 574 residues
Chains: 1
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, HCN, FES
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Iron hydrogenase 1 (EC 1.12.7.2)	protein	574	43% helix, 17% strand	P29166

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A
HCN · 2 iron/2 sulfur/3 carbonyl/2 cyanide/water/methylether cluster · ligand · chains A
FES · Fe2/s2 (inorganic) cluster · ligand · chains A
GOL · Glycerol · additive · 3 copies · chains A

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

Pockets

6 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	108	0.80	0.99	29	HCN, SF4
2	681	0.74	0.80	83	empty
3	97	0.39	0.75	13	empty
4	70	0.36	0.77	15	empty
5	69	0.29	0.73	16	empty

Compared structures

3C8Y · 1.39 Angstrom crystal structure of Fe-only hydrogenase · 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 3C8Y · PDBe 3C8Y · UniProt P29166

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