MolNFT v1 · #8272 · protein

Crystal structure of laccase from melanocarpus albomyces in four copper form

1GW0 · Laccase-1: “Crystal structure of laccase from melanocarpus albomyces in four copper form”. X-ray diffraction, 7 ligands (NAG, MAN, BMA), 12 pockets (best druggability 0.85). MolNFT v1 #8272 on GenesisL1: 3D structure, binding sites…

PDB: 1GW0
Type: protein
Length: 1,118 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Laccase-1
EC: 1.10.3.2
UniProt: Q70KY3
Ligands: NAG, MAN, BMA, CU, SO4, OXY, CL
Pockets: 12 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 11% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Laccase-1 (EC 1.10.3.2)	protein	559	11% helix, 38% strand	Q70KY3

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · 10 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B
CU · Copper (II) ion · metal · 8 copies · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains A, B
OXY · Oxygen molecule · ion · 2 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B

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

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	584	0.85	0.90	80	empty
2	104	0.77	0.97	28	empty
3	102	0.77	0.97	30	empty
4	844	0.70	0.76	94	NAG
5	106	0.64	0.89	32	empty

Interfaces

1 interface between chains.

A–B · 786 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 glycan, 6 disulfide (N-glycosylation, disulfide).

Compared structures

1GW0 · Crystal Structure of Laccase from Melanocarpus albomyces in Four Copper Form · the same entry in another collection · chain A against A, TM-score 1.00
Q70KY3 · AlphaFold monomer V2.0 prediction for laccase-1 (Q70KY3) · a predicted model of the same protein · 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 Q70KY3
Elsewhere: RCSB PDB 1GW0 · PDBe 1GW0 · UniProt Q70KY3

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