Research workbench
Crystal structures of phosphonoacetamide ligated T and phosphonoacetamide and malonate ligated R states of aspartate carbamoyltransferase at 2.8-ångströms resolution and neutral P*H
Analyse Crystal structures of phosphonoacetamide ligated T and phosphonoacetamide and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1AT1
- Type
- protein
- Length
- 912 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate carbamoyltransferase, catalytic chain; Aspartate carbamoyltransferase…
- EC
- 2.1.3.2
- UniProt
- P0A786, P0A7F3
- Ligands
- PCT, ZN
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Aspartate carbamoyltransferase, catalytic chain (EC 2.1.3.2) | protein | 310 | 40% helix, 15% strand | P0A786 |
| B, D | Aspartate carbamoyltransferase regulatory chain | protein | 146 | 15% helix, 37% strand | P0A7F3 |
Ligands and binding sites
- PCT · Phosphonoacetamide · ligand · 2 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains B, D
- MLI · Malonate ion · additive · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.65 | 0.87 | 33 | MLI, PCT |
| 2 | 143 | 0.64 | 0.87 | 23 | MLI, PCT |
| 3 | 182 | 0.45 | 0.75 | 28 | empty |
| 4 | 64 | 0.42 | 0.80 | 17 | empty |
| 5 | 120 | 0.39 | 0.75 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 848 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 787 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 772 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 1AT1 · Crystal structures of phosphonoacetamide ligated T and phosphonoacetamide and malonate… · the same entry in another collection · chain D against D, 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 0.94
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 1AT1 · PDBe 1AT1 · UniProt P0A786 · UniProt P0A7F3
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