MolNFT v1 · #70891 · protein
Crystal structure of putative histidinol-phosphate aminotransferase (YP_050345.1) from erwinia carotovora atroseptica SCRI1043 at 1.80 a resolution
3LY1: “Crystal structure of putative histidinol-phosphate aminotransferase (YP_050345.1) from erwinia carotovora…”. X-ray diffraction, 1 ligand (PLP), 20 pockets (best druggability 0.77). MolNFT v1 #70891 on GenesisL1: 3D structure…
- PDB
- 3LY1
- Type
- protein
- Length
- 1,393 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative histidinol-phosphate aminotransferase
- UniProt
- Q6D4Z0
- Ligands
- PLP
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative histidinol-phosphate aminotransferase | protein | 346 | 43% helix, 15% strand | Q6D4Z0 |
| C | Putative histidinol-phosphate aminotransferase | protein | 347 | 44% helix, 15% strand | Q6D4Z0 |
| D | Putative histidinol-phosphate aminotransferase | protein | 354 | 43% helix, 14% strand | Q6D4Z0 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 23 copies · chains A, B, C, D
- CIT · Citric acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.77 | 0.98 | 28 | empty |
| 2 | 86 | 0.76 | 0.98 | 28 | empty |
| 3 | 264 | 0.64 | 0.82 | 40 | PLP, CIT |
| 4 | 253 | 0.64 | 0.82 | 40 | PLP, CIT |
| 5 | 293 | 0.64 | 0.80 | 51 | PLP, CIT |
Interfaces
2 interfaces between chains.
- A–B · 2060 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2036 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 modified (engineered).
Compared structures
- 3LY1 · Crystal structure of Putative histidinol-phosphate aminotransferase (YP_050345.1) from… · 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 Q6D4Z0
- Elsewhere: RCSB PDB 3LY1 · PDBe 3LY1 · UniProt Q6D4Z0
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