MolNFT v1 · #140449 · protein
L-amino acid OXIDASE/MONOOXYGENASE from pseudomonas sp. aiu 813 - L- ornithine complex
5YB7: “L-amino acid OXIDASE/MONOOXYGENASE from pseudomonas sp. aiu 813 - L- ornithine complex”. X-ray diffraction, 2 ligands (ORN, FAD), 20 pockets (best druggability 0.87). MolNFT v1 #140449 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5YB7
- 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
- ORN, FAD
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | L-amino acid OXIDASE/MONOOXYGENASE | protein | 549 | 37% helix, 19% strand | W6JQJ6 |
Ligands and binding sites
- ORN · L-ornithine · ligand · 8 copies · chains A, C, B, D
- 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.87 | 0.96 | 68 | FAD, ORN |
| 2 | 342 | 0.87 | 0.96 | 55 | empty |
| 3 | 351 | 0.87 | 0.96 | 69 | FAD, ORN |
| 4 | 617 | 0.87 | 0.91 | 95 | FAD, ORN |
| 5 | 1038 | 0.86 | 0.87 | 142 | FAD, ORN |
Interfaces
4 interfaces between chains.
- B–D · 2317 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 2296 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1441 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1420 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5YB7 · L-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 - L-ornithine 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 5YB7 · PDBe 5YB7 · UniProt W6JQJ6
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