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Crystal structure of E. COLI hydrogenase-1 in its as-isolated form

Analyse Crystal structure of E. COLI hydrogenase-1 in its as-isolated form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3USE
Type: protein
Length: 1,698 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hydrogenase-1 small chain; Hydrogenase-1 large chain
EC: 1.12.99.6
UniProt: P69739, P0ACD8
Ligands: SF4, F3S, F4S, SF3, FCO, 3NI, MG, LI, SO4, CL
Pockets: 11 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
S, T	Hydrogenase-1 small chain (EC 1.12.99.6)	protein	268	36% helix, 18% strand	P69739
L, M	Hydrogenase-1 large chain (EC 1.12.99.6)	protein	581	43% helix, 17% strand	P0ACD8

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 2 copies · chains S, T
F3S · FE3-S4 cluster · ligand · 2 copies · chains S, L, T, M
F4S · FE4-S3 cluster · ligand · 2 copies · chains S, L, T, M
SF3 · FE4-S3 cluster · ligand · 2 copies · chains S, L, T, M
FCO · Carbonmonoxide-(dicyano) iron · ligand · 2 copies · chains L, M
3NI · Nickel (III) ion · metal · 2 copies · chains L, M
MG · Magnesium ion · metal · 2 copies · chains L, M
LI · Lithium ion · metal · 2 copies · chains L, M
SO4 · Sulfate ion · ion · 6 copies · chains S, L, T, M
CL · Chloride ion · ion · 3 copies · chains S, T, M
LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains S, T
GOL · Glycerol · additive · 2 copies · chains L

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

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1131	0.81	0.82	90	empty
2	92	0.60	0.87	21	LMT
3	96	0.58	0.85	19	LMT
4	136	0.46	0.77	35	empty
5	143	0.45	0.76	27	empty

Interfaces

6 interfaces between chains.

T–M · 4058 Å² buried · 66 hydrogen bonds · protein-protein
S–L · 3977 Å² buried · 67 hydrogen bonds · protein-protein
S–M · 855 Å² buried · 6 hydrogen bonds · protein-protein
L–T · 830 Å² buried · 9 hydrogen bonds · protein-protein
S–T · 685 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

P0ACD8 · AlphaFold monomer V2.0 prediction for hydrogenase-1 large chain (P0ACD8) · a predicted model of the same protein · chain L against A, TM-score 1.00
P69739 · AlphaFold monomer V2.0 prediction for hydrogenase-1 small chain (P69739) · a predicted model of the same protein · chain S 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 P69739
Every structure of UniProt P0ACD8
Elsewhere: RCSB PDB 3USE · PDBe 3USE · UniProt P69739 · UniProt P0ACD8

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