Research workbench

Azurin mutant M121A-azide

Analyse Azurin mutant M121A-azide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2TSB
Type: protein
Length: 512 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Azurin azide
UniProt: P00282
Ligands: CU, AZI
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Azurin azide	protein	128	14% helix, 34% strand	P00282

Ligands and binding sites

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

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	320	0.76	0.87	32	empty
2	244	0.70	0.86	33	empty
3	215	0.64	0.84	41	empty
4	194	0.57	0.80	32	empty

Interfaces

6 interfaces between chains.

B–D · 520 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 515 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 402 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 374 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 370 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2TSB · Azurin mutant M121A-azide · 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 2TSB · PDBe 2TSB · UniProt P00282

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