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[nife]-hydrogenase (hyb-type) from citrobacter sp. S-77 in an H2- reduced condition

Analyse [nife]-hydrogenase (hyb-type) from citrobacter sp. S-77 in an H2- reduced… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XVB
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: SF4, NFU, F3S, MG
Pockets: 12 · 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	44% helix, 18% strand	—
S, T	[nife]-hydrogenase 2 small subunit	protein	268	37% helix, 15% strand	—

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 4 copies · chains S, L, T, M
NFU · formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) · ligand · 2 copies · chains L, M
F3S · FE3-S4 cluster · ligand · 2 copies · chains L, S, M, T
MG · Magnesium ion · metal · 2 copies · chains L, M
GOL · Glycerol · additive · 4 copies · chains L, T, M

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

Pockets

12 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	193	0.83	0.98	52	empty
2	782	0.81	0.84	62	empty
3	105	0.77	0.96	36	empty
4	112	0.77	0.95	23	empty
5	111	0.54	0.83	23	GOL

Interfaces

6 interfaces between chains.

M–T · 3746 Å² buried · 56 hydrogen bonds · protein-protein
L–S · 3740 Å² buried · 58 hydrogen bonds · protein-protein
L–T · 788 Å² buried · 5 hydrogen bonds · protein-protein
S–M · 764 Å² buried · 5 hydrogen bonds · protein-protein
S–T · 754 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

5XVB · [NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 in an H2-reduced condition · 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 5XVB · PDBe 5XVB

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