MolNFT v1 · #40148 · protein

A high-dose crystal structure of a recombinant melanocarbus albomyces laccase

2IH9 · Laccase-1: “A high-dose crystal structure of a recombinant melanocarbus albomyces laccase”. X-ray diffraction, 5 ligands (NAG, BMA, CU), 13 pockets (best druggability 0.86). MolNFT v1 #40148 on GenesisL1: 3D structure, binding sites…

PDB: 2IH9
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, BMA, CU, SO4, CL
Pockets: 13 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 12% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Laccase-1 (EC 1.10.3.2)	protein	559	12% helix, 38% strand	Q70KY3

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 4 copies · chains A
CU · Copper (II) ion · metal · 8 copies · chains A, B
SO4 · Sulfate ion · ion · 3 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

13 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	488	0.86	0.92	66	empty
2	91	0.76	0.97	28	empty
3	896	0.72	0.77	83	NAG
4	119	0.72	0.92	33	empty
5	105	0.59	0.86	31	empty

Interfaces

1 interface between chains.

A–B · 793 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 glycan, 6 disulfide (N-glycosylation, disulfide).

Compared structures

2IH9 · A high-dose crystal structure of a recombinant Melanocarbus albomyces laccase · 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 2IH9 · PDBe 2IH9 · UniProt Q70KY3

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