Research workbench
Aspartate transcarbamoylase complexed with N-phosphonacetyl-L- aspartate (pala)
Analyse Aspartate transcarbamoylase complexed with N-phosphonacetyl-L- aspartate (pala) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D09
- Type
- protein
- Length
- 926 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate carbamoyltransferase catalytic chain; Aspartate carbamoyltransferase regulatory…
- EC
- 2.1.3.2
- UniProt
- P0A786, P0A7F3
- Ligands
- PAL, ZN
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Aspartate carbamoyltransferase catalytic chain (EC 2.1.3.2) | protein | 310 | 39% helix, 16% strand | P0A786 |
| B, D | Aspartate carbamoyltransferase regulatory chain | protein | 153 | 10% helix, 35% strand | P0A7F3 |
Ligands and binding sites
- PAL · N-(phosphonacetyl)-L-aspartic acid · ligand · 2 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.64 | 0.78 | 43 | empty |
| 2 | 130 | 0.63 | 0.87 | 29 | PAL |
| 3 | 129 | 0.62 | 0.87 | 23 | PAL |
| 4 | 280 | 0.58 | 0.78 | 35 | empty |
| 5 | 132 | 0.42 | 0.76 | 27 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1051 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 855 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 783 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1D09 · Aspartate transcarbamoylase complexed with N-phosphonacetyl-L-aspartate (pala) · 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 A against A, TM-score 0.96
- P0A7F3 · AlphaFold monomer V2.0 prediction for aspartate carbamoyltransferase regulatory chain… · a predicted model of the same protein · chain B against A, TM-score 0.91
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
- Every structure of UniProt P0A7F3
- Elsewhere: RCSB PDB 1D09 · PDBe 1D09 · UniProt P0A786 · UniProt P0A7F3
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