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Crystal structure of a putative thiol-disulfide oxidoreductase from bacteroides vulgatus (target nysgrc-011676), space group P21221

Analyse Crystal structure of a putative thiol-disulfide oxidoreductase from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KA0
Type: protein
Length: 565 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative thiol-disulfide oxidoreductase
UniProt: A6L2G8
Ligands: CL
Pockets: 5 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative thiol-disulfide oxidoreductase	protein	143	34% helix, 24% strand	A6L2G8
B	Putative thiol-disulfide oxidoreductase	protein	140	29% helix, 25% strand	A6L2G8
C, D	Putative thiol-disulfide oxidoreductase	protein	141	34% helix, 25% strand	A6L2G8

Ligands and binding sites

CL · Chloride ion · ion · chains B, D

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

Pockets

5 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	1148	0.84	0.85	110	empty
2	414	0.64	0.78	43	empty
3	426	0.61	0.76	38	empty
4	352	0.55	0.75	45	empty
5	56	0.29	0.74	13	empty

Interfaces

6 interfaces between chains.

A–C · 793 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 691 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 575 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 521 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 287 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4KA0 · Crystal structure of a putative thiol-disulfide oxidoreductase from Bacteroides vulgatus… · 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 A6L2G8
Elsewhere: RCSB PDB 4KA0 · PDBe 4KA0 · UniProt A6L2G8

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