MolNFT v1 · #35109 · protein
Crystal structure of L-glutamate oxidase from streptomyces sp. X-119-6
2E1M: “Crystal structure of L-glutamate oxidase from streptomyces sp. X-119-6”. X-ray diffraction, 2 ligands (FAD, PO4), 10 pockets (best druggability 0.87). MolNFT v1 #35109 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2E1M
- Type
- protein
- Length
- 597 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-glutamate oxidase
- EC
- 1.4.3.11
- UniProt
- Q8L3C7
- Ligands
- FAD, PO4
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-glutamate oxidase (EC 1.4.3.11) | protein | 356 | 36% helix, 20% strand | Q8L3C7 |
| B | L-glutamate oxidase (EC 1.4.3.11) | protein | 90 | 39% helix, 24% strand | Q8L3C7 |
| C | L-glutamate oxidase (EC 1.4.3.11) | protein | 151 | 35% helix, 21% strand | Q8L3C7 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1186 | 0.87 | 0.88 | 117 | FAD |
| 2 | 190 | 0.80 | 0.95 | 31 | empty |
| 3 | 55 | 0.52 | 0.87 | 13 | empty |
| 4 | 163 | 0.46 | 0.76 | 23 | empty |
| 5 | 201 | 0.46 | 0.74 | 35 | PO4 |
Interfaces
3 interfaces between chains.
- A–C · 4015 Ų buried · 60 hydrogen bonds · protein-protein
- B–C · 3409 Ų buried · 66 hydrogen bonds · protein-protein
- A–B · 1771 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 2E1M · Crystal Structure of L-Glutamate Oxidase from Streptomyces sp. X-119-6 · 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 Q8L3C7
- Elsewhere: RCSB PDB 2E1M · PDBe 2E1M · UniProt Q8L3C7
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