MolNFT v1 · #153784 · protein
Crystal structure of S. pombe aspartate aminotransferase
6JPK · Aspartate aminotransferase, cytoplasmic: “Crystal structure of S. pombe aspartate aminotransferase”. X-ray diffraction, 1 ligand (PO4), 8 pockets (best druggability 0.75). MolNFT v1 #153784 on GenesisL1: 3D structure, binding sites…
- PDB
- 6JPK
- Type
- protein
- Length
- 817 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate aminotransferase, cytoplasmic
- EC
- 2.6.1.1
- UniProt
- O42652
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1) | protein | 409 | 48% helix, 13% strand | O42652 |
| B | Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1) | protein | 408 | 48% helix, 13% strand | O42652 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.75 | 0.80 | 69 | PO4 |
| 2 | 788 | 0.73 | 0.78 | 74 | PO4 |
| 3 | 302 | 0.62 | 0.79 | 31 | empty |
| 4 | 124 | 0.43 | 0.76 | 20 | empty |
| 5 | 104 | 0.43 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3149 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 6JPK · Crystal structure of S. pombe aspartate aminotransferase · the same entry in another collection · chain A against A, TM-score 1.00
- O42652 · AlphaFold monomer V2.0 prediction for aspartate aminotransferase, cytoplasmic (O42652) · a predicted model of the same protein · chain B 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 O42652
- Elsewhere: RCSB PDB 6JPK · PDBe 6JPK · UniProt O42652
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