MolNFT v1 · #150598 · protein

Azurin fom pseudomonas aeruginosa treated with hydrosulfide

6GYI: “Azurin fom pseudomonas aeruginosa treated with hydrosulfide”. X-ray diffraction, 2 ligands (CU, CA), 5 pockets (best druggability 0.67). MolNFT v1 #150598 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6GYI
Type: protein
Length: 509 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Azurin
UniProt: P00282
Ligands: CU, CA
Pockets: 5 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 21% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Azurin	protein	127	21% helix, 34% strand	P00282
C	Azurin	protein	128	21% helix, 34% strand	P00282

Ligands and binding sites

CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
CA · Calcium 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

5 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	328	0.67	0.82	45	empty
2	167	0.60	0.83	31	empty
3	152	0.45	0.76	19	empty
4	172	0.43	0.74	25	CA
5	62	0.32	0.76	16	empty

Interfaces

5 interfaces between chains.

A–B · 377 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 324 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 312 Å² buried · 1 hydrogen bond · protein-protein
A–C · 195 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 175 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6GYI · Azurin fom Pseudomonas aeruginosa treated with hydrosulfide · the same entry in another collection · chain C against C, TM-score 1.00
P00282 · AlphaFold monomer V2.0 prediction for azurin (P00282) · a predicted model of the same protein · chain B 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 6GYI · PDBe 6GYI · UniProt P00282

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