MolNFT v1 · #163300 · protein

Copper oxidase from colletotrichum graminicola

6RYX · Kelch domain-containing protein: “Copper oxidase from colletotrichum graminicola”. X-ray diffraction, 2 ligands (NAG, CU), 3 pockets (best druggability 0.63). MolNFT v1 #163300 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6RYX
Type: protein
Length: 626 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kelch domain-containing protein
EC: 1.1.3.7
UniProt: E3Q9X3
Ligands: NAG, CU
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kelch domain-containing protein (EC 1.1.3.7)	protein	626	6% helix, 39% strand	E3Q9X3

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
CU · Copper (II) ion · metal · chains A
PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

3 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	420	0.63	0.77	40	empty
2	104	0.37	0.75	18	empty
3	72	0.34	0.76	20	empty

Modifications

Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

6RYX · Copper oxidase from Colletotrichum graminicola · the same entry in another collection · chain A against A, TM-score 1.00

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 E3Q9X3
Elsewhere: RCSB PDB 6RYX · PDBe 6RYX · UniProt E3Q9X3

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