MolNFT v1 · #79560 · protein
Crystal structure of laccase from steccherinum ochraceum
3T6V: “Crystal structure of laccase from steccherinum ochraceum”. X-ray diffraction, 3 ligands (NAG, CU, SO4), 17 pockets (best druggability 0.90). MolNFT v1 #79560 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3T6V
- Type
- protein
- Length
- 1,485 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laccase
- Ligands
- NAG, CU, SO4
- Pockets
- 17 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Laccase | protein | 495 | 11% helix, 39% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B, C
- CU · Copper (II) ion · metal · 12 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C
- GOL · Glycerol · additive · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.90 | 0.92 | 143 | GOL, SO4 |
| 2 | 128 | 0.67 | 0.89 | 21 | SO4 |
| 3 | 583 | 0.67 | 0.77 | 72 | SO4, GOL |
| 4 | 82 | 0.53 | 0.84 | 24 | GOL |
| 5 | 77 | 0.50 | 0.84 | 14 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 823 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 813 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 809 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 3T6V · Crystal Structure of Laccase from Steccherinum ochraceum · 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 3T6V · PDBe 3T6V
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