MolNFT v1 · #4948 · protein

[nife] hydrogenase from desulfovibrio desulfuricans atcc 27774

1E3D · [nife] hydrogenase small subunit: “[nife] hydrogenase from desulfovibrio desulfuricans atcc 27774”. X-ray diffraction, 6 ligands (F3S, SF4, FSX), 8 pockets (best druggability 0.79). MolNFT v1 #4948 on GenesisL1: 3D structure…

PDB: 1E3D
Type: protein
Length: 1,598 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: [nife] hydrogenase small subunit; [nife] hydrogenase large subunit
UniProt: Q9L869, Q9L868
Ligands: F3S, SF4, FSX, FNE, MG, H2S
Pockets: 8 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	[nife] hydrogenase small subunit	protein	262	40% helix, 17% strand	Q9L869
B, D	[nife] hydrogenase large subunit	protein	537	47% helix, 16% strand	Q9L868

Ligands and binding sites

F3S · FE3-S4 cluster · ligand · 2 copies · chains A, B, C, D
SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, C
FSX · Bis-(mu-2-oxo),[(mu-3--sulfido)-bis(mu-2--sulfido)-tris(cys-S)-tri-iron] (aqua)(glu-o)iron(ii) · ligand · 2 copies · chains A, B, C, D
FNE · (mu-sulphido)-bis(mu-cys,s)-[tricarbonyliron-di-(cys,s)nickel(ii)](fe-Ni) · ligand · 2 copies · chains B, D
MG · Magnesium ion · metal · 2 copies · chains B, D
H2S · Hydrosulfuric acid · ion · 4 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1013	0.79	0.80	78	empty
2	99	0.60	0.87	22	empty
3	88	0.58	0.87	22	empty
4	202	0.54	0.78	38	empty
5	94	0.49	0.82	19	empty

Interfaces

4 interfaces between chains.

C–D · 3670 Å² buried · 70 hydrogen bonds · protein-protein
A–B · 3656 Å² buried · 68 hydrogen bonds · protein-protein
A–D · 153 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 81 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

1E3D · [NiFe] Hydrogenase from Desulfovibrio desulfuricans ATCC 27774 · 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 Q9L869
Every structure of UniProt Q9L868
Elsewhere: RCSB PDB 1E3D · PDBe 1E3D · UniProt Q9L869 · UniProt Q9L868

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