MolNFT v1 · #87306 · protein

Crystal structure of spin labelled azurin T21R1.

4BWW: “Crystal structure of spin labelled azurin T21R1.”. X-ray diffraction, 3 ligands (CU, NO3, SO4), 3 pockets (best druggability 0.72). MolNFT v1 #87306 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4BWW
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, SO4
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 34% strand (DSSP).

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

Ligands and binding sites

CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
NO3 · Nitrate ion · ion · 5 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 5 copies · chains B, C, D
GOL · Glycerol · additive · 8 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	545	0.72	0.80	59	NO3, GOL
2	65	0.38	0.79	20	NO3, GOL
3	59	0.29	0.74	13	empty

Interfaces

5 interfaces between chains.

A–B · 703 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 673 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 472 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 122 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 116 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

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

Compared structures

4BWW · Crystal structure of spin labelled azurin T21R1. · 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 4BWW · PDBe 4BWW · UniProt P00282

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