MolNFT v1 · #151974 · protein
Bilirubin oxidase from myrothecium verrucaria, mutant W396F
6I3L: “Bilirubin oxidase from myrothecium verrucaria, mutant W396F”. X-ray diffraction, 5 ligands (NAG, BMA, CU), 7 pockets (best druggability 0.60). MolNFT v1 #151974 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6I3L
- Type
- protein
- Length
- 1,068 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bilirubin oxidase
- EC
- 1.3.3.5
- UniProt
- Q12737
- Ligands
- NAG, BMA, CU, NA, OXY
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bilirubin oxidase (EC 1.3.3.5) | protein | 534 | 11% helix, 39% strand | Q12737 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CU · Copper (II) ion · metal · 8 copies · chains A, B
- NA · Sodium ion · metal · chains B
- OXY · Oxygen molecule · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
- SIN · Succinic acid · additive · 4 copies · chains A, B
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.60 | 0.75 | 49 | GOL |
| 2 | 373 | 0.54 | 0.74 | 42 | empty |
| 3 | 175 | 0.48 | 0.76 | 25 | empty |
| 4 | 166 | 0.46 | 0.76 | 18 | empty |
| 5 | 66 | 0.40 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 458 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
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 Q12737
- Elsewhere: RCSB PDB 6I3L · PDBe 6I3L · UniProt Q12737
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