MolNFT v1 · #25313 · protein

Structure of electron transfer (cobalt-protein)

1VLX · Azurin: “Structure of electron transfer (cobalt-protein)”. X-ray diffraction, 1 ligand (CO), 5 pockets (best druggability 0.75). MolNFT v1 #25313 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VLX
Type: protein
Length: 512 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Azurin
UniProt: P00282
Ligands: CO
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Azurin	protein	128	15% helix, 34% strand	P00282

Ligands and binding sites

CO · Cobalt (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	235	0.75	0.90	35	empty
2	291	0.69	0.84	37	empty
3	64	0.69	0.96	19	empty
4	298	0.64	0.81	47	empty
5	239	0.60	0.80	45	empty

Interfaces

6 interfaces between chains.

A–C · 551 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 498 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 430 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 398 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 396 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1VLX · Structure of electron transfer (cobalt-protein) · 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 1VLX · PDBe 1VLX · UniProt P00282

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