Research workbench
Crystal structure of wild-type (wt) human glutamate oxaloacetate transaminase 1 (GOT1)
Analyse Crystal structure of wild-type (wt) human glutamate oxaloacetate transaminase 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DND
- Type
- protein
- Length
- 819 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate aminotransferase, cytoplasmic
- EC
- 2.6.1.1, 2.6.1.3
- UniProt
- P17174
- Ligands
- PLP
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1, 2.6.1.3) | protein | 409 | 46% helix, 13% strand | P17174 |
| B | Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1, 2.6.1.3) | protein | 410 | 46% helix, 13% strand | P17174 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · 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 | 902 | 0.75 | 0.79 | 94 | PLP |
| 2 | 595 | 0.73 | 0.80 | 59 | PLP |
| 3 | 124 | 0.72 | 0.93 | 28 | empty |
| 4 | 51 | 0.46 | 0.85 | 15 | empty |
| 5 | 76 | 0.44 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3242 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
- 6DND · Crystal structure of wild-type (WT) human Glutamate oxaloacetate transaminase 1 (GOT1) · the same entry in another collection · chain A against A, TM-score 1.00
- P17174 · AlphaFold monomer V2.0 prediction for aspartate aminotransferase, cytoplasmic (P17174) · a predicted model of the same protein · chain A 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 P17174
- Elsewhere: RCSB PDB 6DND · PDBe 6DND · UniProt P17174
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