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Crystal structure of the oxidized form of ni-fe hydrogenase

Analyse Crystal structure of the oxidized form of ni-fe hydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2FRV
Type: protein
Length: 4,746 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Periplasmic hydrogenase
EC: 1.18.99.1
UniProt: P12943, P12944
Ligands: SF4, F3S, FCO, NI, MG, O
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
S, A, C, E, G, I	Periplasmic hydrogenase (EC 1.18.99.1)	protein	261	40% helix, 16% strand	P12943
L, B, D, F, H, J	Periplasmic hydrogenase (EC 1.18.99.1)	protein	530	48% helix, 16% strand	P12944

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 12 copies · chains S, L, A, B, C, D, E, F, G, H, I, J
F3S · FE3-S4 cluster · ligand · 6 copies · chains S, L, A, B, C, D, E, F, G, H, I, J
FCO · Carbonmonoxide-(dicyano) iron · ligand · 6 copies · chains L, B, D, F, H, J
NI · Nickel (II) ion · metal · 6 copies · chains L, B, D, F, H, J
MG · Magnesium ion · metal · 6 copies · chains L, B, D, F, H, J
O · Oxygen atom · ion · 6 copies · chains L, B, D, F, H, J

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	234	0.82	0.94	58	empty
2	238	0.82	0.94	56	empty
3	227	0.81	0.93	57	empty
4	216	0.80	0.93	50	empty
5	201	0.80	0.93	41	empty

Interfaces

20 interfaces between chains.

C–D · 3584 Å² buried · 61 hydrogen bonds · protein-protein
I–J · 3583 Å² buried · 61 hydrogen bonds · protein-protein
E–F · 3583 Å² buried · 61 hydrogen bonds · protein-protein
A–B · 3579 Å² buried · 61 hydrogen bonds · protein-protein
G–H · 3578 Å² buried · 61 hydrogen bonds · protein-protein

Compared structures

2FRV · Crystal structure of the oxidized form of ni-fe hydrogenase · the same entry in another collection · chain J against J, 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 P12943
Every structure of UniProt P12944
Elsewhere: RCSB PDB 2FRV · PDBe 2FRV · UniProt P12943 · UniProt P12944

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