MolNFT v1 · #121668 · protein

Azurin T30R1, crystal form I

5I26: “Azurin T30R1, crystal form I”. X-ray diffraction, 1 ligand (CU), 5 pockets (best druggability 0.71). MolNFT v1 #121668 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5I26
Type: protein
Length: 508 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Azurin
UniProt: P00282
Ligands: CU
Pockets: 5 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Azurin	protein	128	20% helix, 34% strand	P00282
C	Azurin	protein	125	19% helix, 34% strand	P00282
D	Azurin	protein	127	17% helix, 30% strand	P00282

Ligands and binding sites

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

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	51	0.71	0.98	16	empty
2	223	0.64	0.83	35	empty
3	253	0.63	0.82	45	empty
4	202	0.62	0.83	40	empty
5	161	0.60	0.83	37	empty

Interfaces

6 interfaces between chains.

A–C · 526 Å² buried · 1 hydrogen bond · protein-protein
C–D · 476 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 455 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 416 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 391 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified, 3 disulfide (nonstandard, disulfide).

Compared structures

5I26 · Azurin T30R1, crystal form I · 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 5I26 · PDBe 5I26 · UniProt P00282

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.