MolNFT v1 · #135209 · protein
Crystal structure of L-amino acid oxidase from bothrops atrox
5TS5 · Amine oxidase: “Crystal structure of L-amino acid oxidase from bothrops atrox”. X-ray diffraction, 4 ligands (FAD, NAG, FUC), 18 pockets (best druggability 0.89). MolNFT v1 #135209 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5TS5
- Type
- protein
- Length
- 1,923 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amine oxidase
- EC
- 1.4.3.-
- UniProt
- A0A0S1LJ33
- Ligands
- FAD, NAG, FUC, ZN
- Pockets
- 18 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amine oxidase (EC 1.4.3.-) | protein | 483 | 41% helix, 22% strand | A0A0S1LJ33 |
| B | Amine oxidase (EC 1.4.3.-) | protein | 481 | 41% helix, 22% strand | A0A0S1LJ33 |
| C | Amine oxidase (EC 1.4.3.-) | protein | 480 | 40% helix, 22% strand | A0A0S1LJ33 |
| D | Amine oxidase (EC 1.4.3.-) | protein | 479 | 40% helix, 22% strand | A0A0S1LJ33 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, C, A, D
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains C
- ZN · Zinc ion · metal · 11 copies · chains A, B, D, C
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.89 | 0.91 | 132 | FAD |
| 2 | 848 | 0.86 | 0.88 | 108 | FAD |
| 3 | 1171 | 0.85 | 0.86 | 133 | FAD |
| 4 | 1175 | 0.85 | 0.85 | 132 | FAD |
| 5 | 512 | 0.82 | 0.88 | 54 | ZN |
Interfaces
5 interfaces between chains.
- A–B · 2166 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2123 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 368 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 225 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 58 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5TS5 · Crystal structure of L-amino acid oxidase from Bothrops atrox · 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 A0A0S1LJ33
- Elsewhere: RCSB PDB 5TS5 · PDBe 5TS5 · UniProt A0A0S1LJ33
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