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Oxidised soxax complex from rhodovulum sulfidophilum

Analyse Oxidised soxax complex from rhodovulum sulfidophilum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1H31
Type: protein
Length: 1,596 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diheme cytochrome C; Cytochrome C
UniProt: Q939U1, Q939U4
Ligands: HEC
Pockets: 10 · best druggability 0.88

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Diheme cytochrome C	protein	261	38% helix, 14% strand	Q939U1
B, D, F, H	Cytochrome C	protein	138	30% helix, 2% strand	Q939U4

Ligands and binding sites

HEC · Heme C · ligand · 12 copies · chains A, B, C, D, E, F, G, H

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

Pockets

10 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1007	0.88	0.89	110	HEC
2	731	0.83	0.87	81	HEC
3	1090	0.83	0.84	121	HEC
4	777	0.83	0.86	81	HEC
5	112	0.61	0.86	20	HEC

Interfaces

9 interfaces between chains.

C–D · 1309 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1298 Å² buried · 17 hydrogen bonds · protein-protein
G–H · 1291 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 1289 Å² buried · 19 hydrogen bonds · protein-protein
D–E · 488 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 cofactor, 4 modified (heme c attachment, oxidation).

Compared structures

1H31 · Oxidised SoxAX complex from Rhodovulum sulfidophilum · the same entry in another collection · chain H against H, TM-score 1.00
Q939U1 · AlphaFold monomer V2.0 prediction for L-cysteine S-thiosulfotransferase subunit soxa… · a predicted model of the same protein · 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 Q939U1
Every structure of UniProt Q939U4
Elsewhere: RCSB PDB 1H31 · PDBe 1H31 · UniProt Q939U1 · UniProt Q939U4

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