Research workbench
Crystal structure of a putative aminotransferase (TM1131) from thermotoga maritima MSB8 at 1.82 a resolution
Analyse Crystal structure of a putative aminotransferase (TM1131) from thermotoga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VP4
- Type
- protein
- Length
- 836 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase, putative
- UniProt
- Q9X0L5
- Ligands
- PLP, UNL
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminotransferase, putative | protein | 420 | 47% helix, 15% strand | Q9X0L5 |
| B | Aminotransferase, putative | protein | 416 | 48% helix, 15% strand | Q9X0L5 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
- FMT · Formic acid · additive · 27 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.73 | 0.98 | 19 | EDO |
| 2 | 495 | 0.73 | 0.82 | 45 | PLP, UNL, FMT |
| 3 | 65 | 0.73 | 0.97 | 18 | FMT |
| 4 | 552 | 0.71 | 0.80 | 54 | UNL, EDO, FMT |
| 5 | 89 | 0.54 | 0.85 | 19 | FMT |
Interfaces
1 interface between chains.
- A–B · 3408 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified, 2 cofactor (engineered, pyridoxal phosphate Schiff base).
Compared structures
- 1VP4 · Crystal structure of a putative aminotransferase (tm1131) from thermotoga maritima msb8… · 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 Q9X0L5
- Elsewhere: RCSB PDB 1VP4 · PDBe 1VP4 · UniProt Q9X0L5
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