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Dimethyl disulfide inhibited sulfur oxygenase reductase

Analyse Dimethyl disulfide inhibited sulfur oxygenase reductase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QJC
Type: protein
Length: 1,228 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.7
Source: Acidianus ambivalens
Molecule: Sulfur oxygenase/reductase
EC: 1.13.11.55
UniProt: P29082
Ligands: FE
Pockets: 12 · best druggability 0.80

Structure

x-ray diffraction · resolution 1.7 · 1 distinct chain · 36% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Sulfur oxygenase/reductase (EC 1.13.11.55)	protein	307	36% helix, 30% strand	P29082

Ligands and binding sites

FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D

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

Pockets

12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	643	0.80	0.85	93	empty
2	624	0.80	0.85	85	empty
3	566	0.80	0.85	81	empty
4	648	0.80	0.84	92	empty
5	97	0.75	0.95	18	empty

Interfaces

6 interfaces between chains.

C–D · 1288 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1286 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 1283 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 1274 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 14 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (oxidation, nonstandard).

Compared structures

6QJC · Dimethyl disulfide inhibited sulfur oxygenase reductase · the same entry in another collection · chain A against A, TM-score 1.00
P29082 · AlphaFold monomer V2.0 prediction for sulfur OXYGENASE/REDUCTASE (P29082) · 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 P29082
Elsewhere: RCSB PDB 6QJC · PDBe 6QJC · UniProt P29082

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