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[nife]-hydrogenase (hyb-type) from citrobacter sp. S-77 in a ferricyanide-oxidized condition

Analyse [nife]-hydrogenase (hyb-type) from citrobacter sp. S-77 in a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XVC
Type: protein
Length: 1,638 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: [nife]-hydrogenase 2 large subunit; [nife]-hydrogenase 2 small subunit
Ligands: NFV, SF4, F3S, 8JU, MG
Pockets: 13 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, M	[nife]-hydrogenase 2 large subunit	protein	551	45% helix, 18% strand	—
S, T	[nife]-hydrogenase 2 small subunit	protein	268	35% helix, 15% strand	—

Ligands and binding sites

NFV · Ni-Fe oxidized active center · ligand · 2 copies · chains L, M
SF4 · Iron/sulfur cluster · ligand · 2 copies · chains S, T
F3S · FE3-S4 cluster · ligand · 2 copies · chains L, S, M, T
8JU · FE4-S4-O cluster · ligand · 2 copies · chains L, S, M, T
MG · Magnesium ion · metal · 2 copies · chains L, M
PEG · Di(hydroxyethyl)ether · additive · chains L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	196	0.83	0.98	52	empty
2	1047	0.80	0.82	65	empty
3	110	0.77	0.95	23	empty
4	83	0.75	0.97	22	empty
5	75	0.68	0.93	29	empty

Interfaces

6 interfaces between chains.

M–T · 3762 Å² buried · 58 hydrogen bonds · protein-protein
L–S · 3717 Å² buried · 55 hydrogen bonds · protein-protein
L–T · 783 Å² buried · 5 hydrogen bonds · protein-protein
S–M · 766 Å² buried · 5 hydrogen bonds · protein-protein
S–T · 755 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (oxidation).

Compared structures

5XVC · [NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 in a ferricyanide-oxidized… · the same entry in another collection · chain L against L, 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
Elsewhere: RCSB PDB 5XVC · PDBe 5XVC

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