MolNFT v1 · #55518 · protein
Structure of the epsilon-lysine oxidase from marinomonas mediterranea
2YMW · L-lysine 6-oxidase: “Structure of the epsilon-lysine oxidase from marinomonas mediterranea”. X-ray diffraction, 1 ligand (NA), 15 pockets (best druggability 0.68). MolNFT v1 #55518 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2YMW
- Type
- protein
- Length
- 1,365 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lysine 6-oxidase
- EC
- 1.4.3.20
- UniProt
- F2JXJ3
- Ligands
- NA
- Pockets
- 15 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lysine 6-oxidase (EC 1.4.3.20) | protein | 680 | 19% helix, 28% strand | F2JXJ3 |
| B | L-lysine 6-oxidase (EC 1.4.3.20) | protein | 685 | 19% helix, 29% strand | F2JXJ3 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B
- EOH · Ethanol · additive · 71 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.68 | 0.79 | 44 | EOH |
| 2 | 473 | 0.66 | 0.78 | 44 | EOH |
| 3 | 253 | 0.66 | 0.83 | 39 | EOH |
| 4 | 172 | 0.63 | 0.85 | 46 | empty |
| 5 | 240 | 0.58 | 0.79 | 37 | EOH |
Interfaces
1 interface between chains.
- A–B · 1062 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
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 F2JXJ3
- Elsewhere: RCSB PDB 2YMW · PDBe 2YMW · UniProt F2JXJ3
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