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Crystal structure of an ascomycete fungal laccase from thielavia arenaria
Analyse Crystal structure of an ascomycete fungal laccase from thielavia arenaria in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PPS
- Type
- protein
- Length
- 2,256 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laccase
- EC
- 1.10.3.2
- Ligands
- NAG, MAN, BMA, CU, OXY
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Laccase (EC 1.10.3.2) | protein | 564 | 13% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 34 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A, B, D
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains A, B, C, D
- CU · Copper (II) ion · metal · 16 copies · chains A, B, C, D
- OXY · Oxygen molecule · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.83 | 0.87 | 98 | empty |
| 2 | 776 | 0.83 | 0.86 | 107 | empty |
| 3 | 869 | 0.72 | 0.77 | 91 | NAG |
| 4 | 572 | 0.69 | 0.78 | 73 | empty |
| 5 | 354 | 0.62 | 0.78 | 44 | empty |
Interfaces
5 interfaces between chains.
- C–D · 691 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 680 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 94 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 73 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 23 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 3PPS · Crystal structure of an ascomycete fungal laccase from Thielavia arenaria · 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 3PPS · PDBe 3PPS
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