MolNFT v1 · #76140 · protein
Crystal structure of phosphoserine aminotransferase from yersinia pestis CO92
3QBO: “Crystal structure of phosphoserine aminotransferase from yersinia pestis CO92”. X-ray diffraction, 1 ligand (PLP), 9 pockets (best druggability 0.71). MolNFT v1 #76140 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3QBO
- Type
- protein
- Length
- 717 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoserine aminotransferase
- EC
- 2.6.1.52
- Ligands
- PLP
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoserine aminotransferase (EC 2.6.1.52) | protein | 358 | 39% helix, 18% strand | — |
| B | Phosphoserine aminotransferase (EC 2.6.1.52) | protein | 359 | 40% helix, 18% strand | — |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.71 | 0.98 | 18 | empty |
| 2 | 543 | 0.69 | 0.79 | 49 | PLP |
| 3 | 485 | 0.68 | 0.79 | 45 | PLP |
| 4 | 122 | 0.49 | 0.80 | 28 | empty |
| 5 | 113 | 0.46 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2211 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 3QBO · Crystal structure of phosphoserine aminotransferase from Yersinia pestis CO92 · 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
- Elsewhere: RCSB PDB 3QBO · PDBe 3QBO
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