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Crystal structure of the schiff base intermediate of L-lys epsilon- oxidase from marinomonas mediterranea with L-lys
Analyse Crystal structure of the schiff base intermediate of L-lys epsilon- oxidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WEV
- Type
- protein
- Length
- 1,361 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
- LYS, SO4
- Pockets
- 15 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lysine 6-oxidase (EC 1.4.3.20) | protein | 680 | 20% helix, 28% strand | F2JXJ3 |
| B | L-lysine 6-oxidase (EC 1.4.3.20) | protein | 681 | 20% helix, 28% strand | F2JXJ3 |
Ligands and binding sites
- LYS · Lysine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B
- DIO · 1,4-diethylene dioxide · additive · 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 | 464 | 0.67 | 0.79 | 47 | EDO |
| 2 | 481 | 0.67 | 0.78 | 46 | EDO |
| 3 | 391 | 0.60 | 0.76 | 48 | LYS, SO4 |
| 4 | 155 | 0.59 | 0.83 | 34 | EDO |
| 5 | 110 | 0.59 | 0.86 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 975 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, cofactor).
Compared structures
- 3WEV · Crystal structure of the Schiff base intermediate of L-Lys epsilon-oxidase from… · the same entry in another collection · chain A against A, TM-score 1.00
- F2JXJ3 · AlphaFold monomer V2.0 prediction for L-lysine 6-oxidase (F2JXJ3) · a predicted model of the same protein · 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 F2JXJ3
- Elsewhere: RCSB PDB 3WEV · PDBe 3WEV · UniProt F2JXJ3
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