Research workbench
The isolated, unregulated catalytic trimer of aspartate transcarbamoylase complexed with bisubstrate analog pala (N-(phosphonacetyl)-L-aspartate)
Analyse The isolated, unregulated catalytic trimer of aspartate transcarbamoylase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EKX
- Type
- protein
- Length
- 926 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate transcarbamoylase
- EC
- 2.1.3.2
- UniProt
- P0A786
- Ligands
- PAL, CA
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate transcarbamoylase (EC 2.1.3.2) | protein | 310 | 40% helix, 15% strand | P0A786 |
| B, C | Aspartate transcarbamoylase (EC 2.1.3.2) | protein | 308 | 42% helix, 16% strand | P0A786 |
Ligands and binding sites
- PAL · N-(phosphonacetyl)-L-aspartic acid · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1189 | 0.83 | 0.85 | 123 | empty |
| 2 | 89 | 0.76 | 0.98 | 29 | PAL |
| 3 | 82 | 0.74 | 0.98 | 31 | PAL |
| 4 | 72 | 0.73 | 0.98 | 30 | PAL |
| 5 | 63 | 0.40 | 0.80 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1134 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1132 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1099 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1EKX · The isolated, unregulated catalytic trimer of aspartate transcarbamoylase complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A786 · AlphaFold monomer V2.0 prediction for aspartate carbamoyltransferase catalytic subunit… · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P0A786
- Elsewhere: RCSB PDB 1EKX · PDBe 1EKX · UniProt P0A786
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