MolNFT v1 · #139424 · protein

Crystal structure of NAD+-reducing [nife]-hydrogenase in the H2- reduced state

5XFA · NAD-reducing hydrogenase: “Crystal structure of NAD+-reducing [nife]-hydrogenase in the H2- reduced state”. X-ray diffraction, 5 ligands (SF4, FES, FCO), 20 pockets (best druggability 0.89). MolNFT v1 #139424 on GenesisL1: 3D…

PDB: 5XFA
Type: protein
Length: 2,879 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NAD-reducing hydrogenase
UniProt: A0A077L6X8, A0A077L885, A0A077L7R5, A0A077LAI5
Ligands: SF4, FES, FCO, NI, MG
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 6 distinct chains · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NAD-reducing hydrogenase	protein	581	45% helix, 15% strand	A0A077L6X8
B, F	NAD-reducing hydrogenase	protein	234	26% helix, 16% strand	A0A077L885
C, G	NAD-reducing hydrogenase	protein	178	38% helix, 22% strand	A0A077L7R5
D	NAD-reducing hydrogenase	protein	452	50% helix, 19% strand	A0A077LAI5
E	NAD-reducing hydrogenase	protein	571	47% helix, 15% strand	A0A077L6X8
H	NAD-reducing hydrogenase	protein	451	50% helix, 19% strand	A0A077LAI5

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 8 copies · chains A, B, C, D, E, F, G, H
FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains B, F
FCO · Carbonmonoxide-(dicyano) iron · ligand · 2 copies · chains D, H
NI · Nickel (II) ion · metal · 2 copies · chains D, H
MG · Magnesium ion · metal · 2 copies · chains D, H

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1073	0.89	0.91	146	empty
2	332	0.78	0.89	57	empty
3	79	0.76	0.99	24	empty
4	679	0.75	0.81	63	empty
5	586	0.75	0.82	37	empty

Interfaces

16 interfaces between chains.

C–D · 2861 Å² buried · 47 hydrogen bonds · protein-protein
G–H · 2843 Å² buried · 49 hydrogen bonds · protein-protein
E–F · 1752 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1729 Å² buried · 24 hydrogen bonds · protein-protein
F–G · 1192 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5XFA · Crystal structure of NAD+-reducing [NiFe]-hydrogenase in the H2-reduced state · the same entry in another collection · chain A against A, 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 A0A077L6X8
Every structure of UniProt A0A077L885
Every structure of UniProt A0A077L7R5
Every structure of UniProt A0A077LAI5
Elsewhere: RCSB PDB 5XFA · PDBe 5XFA · UniProt A0A077L6X8 · UniProt A0A077L885 · UniProt A0A077L7R5 · UniProt A0A077LAI5

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