MolNFT v1 · #86521 · protein
The structure of the omega aminotransferase from pseudomonas aeruginosa
4B98 · Beta-alanine--pyruvate transaminase: “The structure of the omega aminotransferase from pseudomonas aeruginosa”. X-ray diffraction, 4 ligands (PXG, PLP, CA), 16 pockets (best druggability 0.85). MolNFT v1 #86521 on GenesisL1: 3D…
- PDB
- 4B98
- Type
- protein
- Length
- 1,763 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-alanine--pyruvate transaminase
- EC
- 2.6.1.18
- UniProt
- Q9I700
- Ligands
- PXG, PLP, CA, CL
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Beta-alanine--pyruvate transaminase (EC 2.6.1.18) | protein | 441 | 40% helix, 18% strand | Q9I700 |
| B | Beta-alanine--pyruvate transaminase (EC 2.6.1.18) | protein | 440 | 40% helix, 18% strand | Q9I700 |
Ligands and binding sites
- PXG · 3-[O-phosphonopyridoxyl]--amino-benzoic acid · ligand · 4 copies · chains A, B, C, D
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, D, B, C
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.85 | 0.96 | 55 | empty |
| 2 | 296 | 0.85 | 0.96 | 52 | empty |
| 3 | 653 | 0.78 | 0.83 | 76 | CL, PXG |
| 4 | 650 | 0.78 | 0.83 | 70 | PXG, CL |
| 5 | 664 | 0.78 | 0.83 | 72 | PXG, CL |
Interfaces
6 interfaces between chains.
- C–D · 6203 Ų buried · 93 hydrogen bonds · protein-protein
- A–B · 6107 Ų buried · 94 hydrogen bonds · protein-protein
- B–C · 952 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 884 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 296 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4B98 · The structure of the omega aminotransferase from Pseudomonas aeruginosa · the same entry in another collection · chain D against D, TM-score 1.00
- Q9I700 · AlphaFold monomer V2.0 prediction for beta-alanine--pyruvate aminotransferase (Q9I700) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9I700
- Elsewhere: RCSB PDB 4B98 · PDBe 4B98 · UniProt Q9I700
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