Research workbench
X-ray crystal structure of the wbpe (wlbe) aminotransferase from pseudomonas aeruginosa as the plp internal aldimine adduct with lysine 185
Analyse X-ray crystal structure of the wbpe (wlbe) aminotransferase from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NYU
- Type
- protein
- Length
- 1,430 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase wbpe
- UniProt
- Q9HZ76
- Ligands
- NA
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminotransferase wbpe | protein | 359 | 43% helix, 16% strand | Q9HZ76 |
| B, C, D | Aminotransferase wbpe | protein | 357 | 42% helix, 16% strand | Q9HZ76 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.80 | 0.89 | 53 | empty |
| 2 | 419 | 0.65 | 0.78 | 37 | empty |
| 3 | 397 | 0.64 | 0.78 | 41 | EDO |
| 4 | 356 | 0.63 | 0.79 | 37 | empty |
| 5 | 356 | 0.63 | 0.78 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2317 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2302 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 809 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 3NYU · X-ray crystal structure of the Wbpe (WlbE) aminotransferase from pseudomonas aeruginosa… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HZ76 · AlphaFold monomer V2.0 prediction for udp-2-acetamido-2-deoxy-3-oxo- D-glucuronate… · 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 Q9HZ76
- Elsewhere: RCSB PDB 3NYU · PDBe 3NYU · UniProt Q9HZ76
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