Research workbench

Iodoacetamide inhibited sulfur oxygenase reductase

Analyse Iodoacetamide 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: 2YAX
Type: protein
Length: 1,842 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sulfur OXYGENASE/REDUCTASE
EC: 1.13.11.55
UniProt: P29082
Ligands: FE
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Sulfur OXYGENASE/REDUCTASE (EC 1.13.11.55)	protein	307	36% helix, 31% strand	P29082

Ligands and binding sites

FE · Fe (III) ion · metal · 6 copies · chains A, B, C, D, E, F

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	900	0.88	0.90	79	empty
2	937	0.88	0.89	86	empty
3	921	0.88	0.89	86	empty
4	640	0.84	0.88	88	empty
5	272	0.83	0.94	42	empty

Interfaces

8 interfaces between chains.

A–B · 2417 Å² buried · 48 hydrogen bonds · protein-protein
C–E · 2417 Å² buried · 48 hydrogen bonds · protein-protein
D–F · 2411 Å² buried · 47 hydrogen bonds · protein-protein
D–E · 1284 Å² buried · 11 hydrogen bonds · protein-protein
B–E · 1268 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 modified (oxidation, alkylation).

Compared structures

2YAX · Iodoacetamide inhibited sulfur oxygenase reductase · the same entry in another collection · chain C against C, 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 2YAX · PDBe 2YAX · UniProt P29082

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