MolNFT v1 · #139953 · protein

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

5XVD · [nife]-hydrogenase 2 large subunit: “[nife]-hydrogenase (hyb-type) from citrobacter sp. S-77 in an air- oxidized condition”. X-ray diffraction, 6 ligands (SF4, NFV, F3S), 17 pockets (best druggability 0.83). MolNFT v1 #139953 on…

PDB: 5XVD
Type: protein
Length: 1,640 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: [nife]-hydrogenase 2 large subunit; Hydrogenase-2 small chain
UniProt: A0A0J1PJ79
Ligands: SF4, NFV, F3S, 8JU, MG, NA
Pockets: 17 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, M	[nife]-hydrogenase 2 large subunit	protein	551	46% helix, 17% strand	—
S, T	Hydrogenase-2 small chain	protein	269	36% helix, 15% strand	A0A0J1PJ79

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 4 copies · chains S, L, T, M
NFV · Ni-Fe oxidized active center · ligand · 2 copies · chains L, M
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
NA · Sodium ion · metal · 2 copies · chains L, M
GOL · Glycerol · additive · 4 copies · chains L, S, M, T

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

Pockets

17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	197	0.83	0.97	56	empty
2	1198	0.79	0.81	80	empty
3	104	0.77	0.96	31	empty
4	86	0.75	0.96	22	empty
5	55	0.73	0.99	23	SF4, 8JU

Interfaces

6 interfaces between chains.

L–S · 3752 Å² buried · 58 hydrogen bonds · protein-protein
M–T · 3730 Å² buried · 58 hydrogen bonds · protein-protein
L–T · 781 Å² buried · 6 hydrogen bonds · protein-protein
S–M · 770 Å² buried · 6 hydrogen bonds · protein-protein
S–T · 745 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (oxidation).

Compared structures

5XVD · [NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 in an air-oxidized condition · the same entry in another collection · chain T against T, 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 A0A0J1PJ79
Elsewhere: RCSB PDB 5XVD · PDBe 5XVD · UniProt A0A0J1PJ79

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