Research workbench
Crystal structure of lacb from trametes sp. AH28-2
Analyse Crystal structure of lacb from trametes sp. AH28-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KW7
- Type
- protein
- Length
- 1,004 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laccase B
- EC
- 1.10.3.2
- UniProt
- Q5I7J0
- Ligands
- NAG, CU
- Pockets
- 10 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Laccase B (EC 1.10.3.2) | protein | 502 | 10% helix, 37% strand | Q5I7J0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- CU · Copper (II) ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.53 | 0.77 | 34 | empty |
| 2 | 201 | 0.52 | 0.77 | 37 | empty |
| 3 | 86 | 0.52 | 0.84 | 20 | empty |
| 4 | 98 | 0.49 | 0.81 | 21 | empty |
| 5 | 95 | 0.42 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 146 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 3KW7 · Crystal structure of LacB from Trametes sp. AH28-2 · 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 Q5I7J0
- Elsewhere: RCSB PDB 3KW7 · PDBe 3KW7 · UniProt Q5I7J0
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