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Azurin dimer, covalently crosslinked through bis-maleimidomethylether

Analyse Azurin dimer, covalently crosslinked through bis-maleimidomethylether in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JVL
Type: protein
Length: 256 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Azurin
UniProt: P00282
Ligands: OPP, CU, NI
Pockets: 2 · best druggability 0.31

Structure

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

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

Ligands and binding sites

OPP · 1-[pyrrol-1-yl-2,5-dione-methoxymethyl]-pyrrole-2,5-dione · ligand · chains A, B
CU · Copper (II) ion · metal · 2 copies · chains A, B
NI · Nickel (II) ion · metal · 2 copies · chains A, B
144 · Tris-hydroxymethyl-methyl-ammonium · additive · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	58	0.31	0.76	11	empty
2	51	0.28	0.75	15	empty

Interfaces

1 interface between chains.

A–B · 494 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).

Compared structures

1JVL · Azurin dimer, covalently crosslinked through bis-maleimidomethylether · the same entry in another collection · chain A against A, 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 1JVL · PDBe 1JVL · UniProt P00282

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