Research workbench
The crystal structure of halomonas elongata amino-transferase
Analyse The crystal structure of halomonas elongata amino-transferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GWI
- Type
- protein
- Length
- 899 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putrescine aminotransferase
- EC
- 2.6.1.-
- UniProt
- E1V913
- Ligands
- PLP, CL
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putrescine aminotransferase (EC 2.6.1.-) | protein | 449 | 45% helix, 18% strand | E1V913 |
| B | Putrescine aminotransferase (EC 2.6.1.-) | protein | 450 | 45% helix, 18% strand | E1V913 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.76 | 0.84 | 55 | PLP |
| 2 | 556 | 0.75 | 0.82 | 77 | PLP |
| 3 | 69 | 0.52 | 0.86 | 20 | empty |
| 4 | 76 | 0.51 | 0.84 | 22 | EDO |
| 5 | 99 | 0.36 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 5501 Ų buried · 76 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6GWI · The crystal structure of Halomonas elongata amino-transferase · 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 E1V913
- Elsewhere: RCSB PDB 6GWI · PDBe 6GWI · UniProt E1V913
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