MolNFT v1 · #148458 · protein
Crystal structure of the prephenate aminotransferase from rhizobium meliloti
6F77 · Aspartate aminotransferase a: “Crystal structure of the prephenate aminotransferase from rhizobium meliloti”. X-ray diffraction, 1 ligand (PLP), 15 pockets (best druggability 0.77). MolNFT v1 #148458 on GenesisL1: 3D structure…
- PDB
- 6F77
- Type
- protein
- Length
- 2,375 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate aminotransferase a
- EC
- 2.6.1.1
- UniProt
- Q02635
- Ligands
- PLP
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F | Aspartate aminotransferase a (EC 2.6.1.1) | protein | 399 | 47% helix, 14% strand | Q02635 |
| C | Aspartate aminotransferase a (EC 2.6.1.1) | protein | 380 | 46% helix, 15% strand | Q02635 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 5 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.77 | 0.79 | 89 | PLP |
| 2 | 1133 | 0.74 | 0.77 | 112 | PLP |
| 3 | 775 | 0.74 | 0.79 | 68 | PLP |
| 4 | 763 | 0.73 | 0.78 | 72 | empty |
| 5 | 569 | 0.71 | 0.79 | 49 | PLP |
Interfaces
8 interfaces between chains.
- C–D · 2663 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2585 Ų buried · 44 hydrogen bonds · protein-protein
- E–F · 2575 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 333 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 43 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor, 1 modified (pyridoxal phosphate Schiff base, cofactor).
Compared structures
- 6F77 · Crystal structure of the prephenate aminotransferase from Rhizobium meliloti · the same entry in another collection · chain E against E, TM-score 1.00
- Q02635 · AlphaFold monomer V2.0 prediction for ASPARTATE/PREPHENATE aminotransferase (Q02635) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q02635
- Elsewhere: RCSB PDB 6F77 · PDBe 6F77 · UniProt Q02635
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