Research workbench
Crystal structure of aminotransferase-like protein from variovorax paradoxus
Analyse Crystal structure of aminotransferase-like protein from variovorax paradoxus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Z79
- Type
- protein
- Length
- 1,793 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase, class 4
- UniProt
- T1XIY1
- Ligands
- PLP, PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminotransferase, class 4 | protein | 300 | 29% helix, 30% strand | T1XIY1 |
| B | Aminotransferase, class 4 | protein | 306 | 29% helix, 29% strand | T1XIY1 |
| C | Aminotransferase, class 4 | protein | 297 | 29% helix, 30% strand | T1XIY1 |
| D | Aminotransferase, class 4 | protein | 294 | 29% helix, 30% strand | T1XIY1 |
| E | Aminotransferase, class 4 | protein | 300 | 29% helix, 30% strand | T1XIY1 |
| F | Aminotransferase, class 4 | protein | 296 | 29% helix, 30% strand | T1XIY1 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.86 | 0.89 | 62 | empty |
| 2 | 174 | 0.81 | 0.97 | 44 | PLP, PO4 |
| 3 | 523 | 0.78 | 0.85 | 68 | PLP, PO4, PEG |
| 4 | 548 | 0.74 | 0.82 | 54 | PLP, PO4 |
| 5 | 523 | 0.73 | 0.82 | 60 | PLP, PO4 |
Interfaces
12 interfaces between chains.
- A–B · 2647 Ų buried · 40 hydrogen bonds · protein-protein
- E–F · 2510 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2500 Ų buried · 32 hydrogen bonds · protein-protein
- C–E · 603 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 600 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7Z79 · Crystal structure of aminotransferase-like protein from Variovorax paradoxus · 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 T1XIY1
- Elsewhere: RCSB PDB 7Z79 · PDBe 7Z79 · UniProt T1XIY1
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