Research workbench

Co-azurin from pseudomonas aeruginosa treated with hydrosulfide

Analyse Co-azurin from pseudomonas aeruginosa treated with hydrosulfide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IAV
Type: protein
Length: 508 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Azurin
UniProt: P00282
Ligands: CO, CA
Pockets: 6 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 19% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Azurin	protein	127	19% helix, 34% strand	P00282

Ligands and binding sites

CO · Cobalt (II) ion · metal · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 3 copies · chains A, B, C

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	398	0.68	0.80	37	empty
2	352	0.66	0.80	44	empty
3	83	0.37	0.76	19	empty
4	107	0.33	0.72	22	empty
5	57	0.29	0.74	16	empty

Interfaces

5 interfaces between chains.

A–B · 369 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 340 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 327 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 216 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 77 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6IAV · Co-azurin from pseudomonas aeruginosa treated with hydrosulfide · the same entry in another collection · chain D against D, TM-score 1.00
P00282 · AlphaFold monomer V2.0 prediction for azurin (P00282) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P00282
Elsewhere: RCSB PDB 6IAV · PDBe 6IAV · UniProt P00282

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