Research workbench

PM1 mutant, 7D5

Analyse PM1 mutant, 7D5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6H5Y
Type: protein
Length: 972 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.3
Source: Aspergillus oryzae
Molecule: Laccase
Ligands: NAG, CU, SO4
Pockets: 7 · best druggability 0.80

Structure

x-ray diffraction · resolution 2.3 · 2 distinct chains · 10% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Laccase	protein	483	11% helix, 39% strand	—
B	Laccase	protein	489	10% helix, 38% strand	—

Ligands and binding sites

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

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	993	0.80	0.81	93	NAG
2	74	0.54	0.86	15	empty
3	95	0.50	0.82	17	empty
4	192	0.50	0.77	34	empty
5	96	0.42	0.78	22	empty

Interfaces

1 interface between chains.

A–B · 427 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

6H5Y · PM1 mutant, 7D5 · 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 6H5Y · PDBe 6H5Y

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