MolNFT v1 · #141276 · protein

Crystal structure of laccase from cerrena sp. RSD1

5Z22: “Crystal structure of laccase from cerrena sp. RSD1”. X-ray diffraction, 4 ligands (NAG, CU, SO4), 5 pockets (best druggability 0.55). MolNFT v1 #141276 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5Z22
Type: protein
Length: 494 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Laccase
EC: 1.10.3.2
Ligands: NAG, CU, SO4, OXY
Pockets: 5 · best druggability 0.55

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Laccase (EC 1.10.3.2)	protein	494	12% helix, 38% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
CU · Copper (II) ion · metal · 4 copies · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A
OXY · Oxygen molecule · ion · chains A
GOL · Glycerol · additive · chains A

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

Pockets

5 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	117	0.55	0.83	17	GOL
2	215	0.49	0.75	33	empty
3	85	0.42	0.79	18	empty
4	113	0.37	0.74	24	empty
5	62	0.31	0.75	15	empty

Modifications

Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

5Z22 · Crystal Structure of Laccase from Cerrena sp. RSD1 · 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
Elsewhere: RCSB PDB 5Z22 · PDBe 5Z22

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