MolNFT v1 · #135538 · protein
X-ray structure of the wlarg aminotransferase from campylobacter jejuni, internal plp-aldimine
5U20 · Putative aminotransferase: “X-ray structure of the wlarg aminotransferase from campylobacter jejuni, internal plp-aldimine”. X-ray diffraction, 2 ligands (NA, CL), 13 pockets (best druggability 0.78). MolNFT v1 #135538 on GenesisL1…
- PDB
- 5U20
- Type
- protein
- Length
- 1,443 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative aminotransferase
- UniProt
- Q9ALS9
- Ligands
- NA, CL
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative aminotransferase | protein | 361 | 43% helix, 17% strand | Q9ALS9 |
| D | Putative aminotransferase | protein | 360 | 43% helix, 17% strand | Q9ALS9 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.78 | 0.83 | 46 | empty |
| 2 | 588 | 0.77 | 0.84 | 84 | empty |
| 3 | 529 | 0.74 | 0.82 | 47 | empty |
| 4 | 502 | 0.73 | 0.81 | 46 | empty |
| 5 | 431 | 0.72 | 0.82 | 40 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2491 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2425 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 801 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 5U20 · X-ray structure of the WlaRG aminotransferase from Campylobacter jejuni, internal… · 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 Q9ALS9
- Elsewhere: RCSB PDB 5U20 · PDBe 5U20 · UniProt Q9ALS9
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