MolNFT v1 · #78095 · protein

Structure of oxidized M98K mutant of amicyanin

3RYM: “Structure of oxidized M98K mutant of amicyanin”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.78). MolNFT v1 #78095 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3RYM
Type: protein
Length: 420 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Amicyanin
UniProt: P22364
Ligands: ZN
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Amicyanin	protein	105	3% helix, 48% strand	P22364

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, C, B, D

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

Pockets

6 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	620	0.78	0.84	70	empty
2	215	0.47	0.74	33	empty
3	128	0.40	0.74	28	empty
4	92	0.38	0.76	25	empty
5	59	0.27	0.73	14	empty

Interfaces

6 interfaces between chains.

A–B · 525 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 492 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 427 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 398 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 99 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3RYM · Structure of Oxidized M98K 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 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 P22364
Elsewhere: RCSB PDB 3RYM · PDBe 3RYM · UniProt P22364

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