MolNFT v1 · #125605 · protein
Recombinant high-redox potential laccase from basidiomycete trametes hirsuta
5LDU · Laccase a: “Recombinant high-redox potential laccase from basidiomycete trametes hirsuta”. X-ray diffraction, 5 ligands (NAG, BMA, MAN), 4 pockets (best druggability 0.57). MolNFT v1 #125605 on GenesisL1: 3D structure, binding sites…
- PDB
- 5LDU
- Type
- protein
- Length
- 499 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laccase a
- UniProt
- A0A0A7M685
- Ligands
- NAG, BMA, MAN, CU, NA
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Laccase a | protein | 499 | 11% helix, 37% strand | A0A0A7M685 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- CU · Copper (II) ion · metal · 4 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.57 | 0.82 | 22 | GOL |
| 2 | 281 | 0.53 | 0.75 | 44 | NA |
| 3 | 122 | 0.45 | 0.78 | 23 | empty |
| 4 | 120 | 0.39 | 0.74 | 19 | empty |
Modifications
Observed in the structure: 5 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 5LDU · Recombinant high-redox potential laccase from Basidiomycete Trametes hirsuta · 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 A0A0A7M685
- Elsewhere: RCSB PDB 5LDU · PDBe 5LDU · UniProt A0A0A7M685
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