Research workbench

Crystal structure of amicyanin substituted with cobalt

Analyse Crystal structure of amicyanin substituted with cobalt in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1T5K
Type: protein
Length: 420 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Amicyanin
UniProt: P22364
Ligands: CO, PO4
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Amicyanin	protein	105	3% helix, 50% strand	P22364

Ligands and binding sites

CO · Cobalt (II) ion · metal · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 5 copies · chains A, B, C

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	566	0.72	0.80	41	empty
2	409	0.67	0.80	37	empty
3	133	0.52	0.81	22	empty

Interfaces

5 interfaces between chains.

A–C · 412 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 293 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 262 Å² buried · 1 hydrogen bond · protein-protein
B–C · 240 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 240 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

1T5K · Crystal structure of amicyanin substituted with cobalt · the same entry in another collection · chain D against D, TM-score 1.00
P22364 · AlphaFold monomer V2.0 prediction for amicyanin (P22364) · a predicted model of the same protein · chain D 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 P22364
Elsewhere: RCSB PDB 1T5K · PDBe 1T5K · UniProt P22364

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