MolNFT v1 · #5037 · protein

Azurin from pseudomonas aeruginosa, reduced form, pH 5.5

1E5Y: “Azurin from pseudomonas aeruginosa, reduced form, pH 5.5”. X-ray diffraction, 2 ligands (CU, NO3), 5 pockets (best druggability 0.72). MolNFT v1 #5037 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1E5Y
Type: protein
Length: 512 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Azurin
UniProt: P00282
Ligands: CU, NO3
Pockets: 5 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Azurin	protein	128	20% helix, 34% strand	P00282

Ligands and binding sites

CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
NO3 · Nitrate ion · ion · chains A

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

Pockets

5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	243	0.72	0.87	34	empty
2	298	0.67	0.83	42	empty
3	61	0.66	0.95	19	empty
4	282	0.62	0.80	46	empty
5	242	0.58	0.79	45	empty

Interfaces

6 interfaces between chains.

A–C · 533 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 512 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 413 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 411 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 394 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1E5Y · Azurin from Pseudomonas aeruginosa, reduced form, pH 5.5 · 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 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 1E5Y · PDBe 1E5Y · UniProt P00282

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