MolNFT v1 · #140450 · protein
L-amino acid OXIDASE/MONOOXYGENASE from pseudomonas sp. aiu 813 - L- arginine complex
5YB8: “L-amino acid OXIDASE/MONOOXYGENASE from pseudomonas sp. aiu 813 - L- arginine complex”. X-ray diffraction, 2 ligands (ARG, FAD), 20 pockets (best druggability 0.88). MolNFT v1 #140450 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5YB8
- Type
- protein
- Length
- 2,196 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-amino acid OXIDASE/MONOOXYGENASE
- UniProt
- W6JQJ6
- Ligands
- ARG, FAD
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | L-amino acid OXIDASE/MONOOXYGENASE | protein | 549 | 36% helix, 20% strand | W6JQJ6 |
Ligands and binding sites
- ARG · Arginine · ligand · 8 copies · chains A, D, B, C
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.88 | 0.91 | 103 | empty |
| 2 | 1165 | 0.88 | 0.89 | 123 | ARG |
| 3 | 711 | 0.86 | 0.90 | 103 | ARG, FAD |
| 4 | 688 | 0.86 | 0.90 | 95 | ARG, FAD |
| 5 | 713 | 0.86 | 0.90 | 100 | ARG, FAD |
Interfaces
4 interfaces between chains.
- A–D · 1904 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1837 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1517 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1510 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5YB8 · L-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 - L-arginine complex · the same entry in another collection · chain D against D, 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 W6JQJ6
- Elsewhere: RCSB PDB 5YB8 · PDBe 5YB8 · UniProt W6JQJ6
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