MolNFT v1 · #75293 · protein

Structure of oxidized P96G mutant of amicyanin

3PLY: “Structure of oxidized P96G mutant of amicyanin”. X-ray diffraction, 4 ligands (CU, NA, K), 4 pockets (best druggability 0.75). MolNFT v1 #75293 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3PLY
Type: protein
Length: 420 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Amicyanin
UniProt: P22364
Ligands: CU, NA, K, PO4
Pockets: 4 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Amicyanin	protein	105	3% helix, 45% strand	P22364

Ligands and binding sites

CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
NA · Sodium ion · metal · 2 copies · chains A
K · Potassium ion · metal · chains C
PO4 · Phosphate ion · ion · 2 copies · chains 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	551	0.75	0.83	77	empty
2	145	0.45	0.76	21	empty
3	82	0.45	0.80	16	empty
4	59	0.35	0.78	13	empty

Interfaces

6 interfaces between chains.

A–B · 424 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 408 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 390 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 328 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 234 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3PLY · Structure of Oxidized P96G Mutant of Amicyanin · 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 A 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 3PLY · PDBe 3PLY · UniProt P22364

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