Research workbench

Pseudomonas aeruginosa E2Q/H83Q/T126H-azurin RE(PHEN)(CO)3

Analyse Pseudomonas aeruginosa E2Q/H83Q/T126H-azurin RE(PHEN)(CO)3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3IBO
Type: protein
Length: 512 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Azurin
UniProt: P00282
Ligands: REP, CU
Pockets: 3 · best druggability 0.71

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	128	19% helix, 34% strand	P00282

Ligands and binding sites

REP · (1,10 phenanthroline)-(tri-carbon monoxide) rhenium (I) · ligand · 4 copies · chains A, B, C, D
CU · Copper (II) 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

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	779	0.71	0.77	102	empty
2	135	0.40	0.74	22	empty
3	140	0.39	0.73	29	empty

Interfaces

5 interfaces between chains.

A–C · 380 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 352 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 258 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 230 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 68 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3IBO · Pseudomonas aeruginosa E2Q/H83Q/T126H-azurin RE(PHEN)(CO)3 · 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 3IBO · PDBe 3IBO · UniProt P00282

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