MolNFT v1 · #20292 · protein
Crystal structure of CTP-ligated T state aspartate transcarbamoylase at 2.5 ångströms resolution: implications for atcase mutants and the mechanism of negative cooperativity
1RAF · Aspartate carbamoyltransferase catalytic chain: “Crystal structure of CTP-ligated T state aspartate transcarbamoylase at 2.5 ångströms resolution…”. X-ray diffraction, 2 ligands (CTP, ZN), 10 pockets (best druggability 0.62). MolNFT…
- PDB
- 1RAF
- 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
- CTP, ZN
- Pockets
- 10 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 21% 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 | 14% helix, 32% strand | P0A7F3 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains B, D
- 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
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.62 | 0.79 | 37 | CTP |
| 2 | 299 | 0.59 | 0.78 | 33 | empty |
| 3 | 280 | 0.58 | 0.78 | 30 | empty |
| 4 | 145 | 0.48 | 0.78 | 22 | empty |
| 5 | 168 | 0.48 | 0.77 | 27 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1156 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 722 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 691 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1RAF · Crystal structure of CTP-ligated T state aspartate transcarbamoylase at 2.5 ångströms… · 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 0.97
- 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 1RAF · PDBe 1RAF · UniProt P0A786 · UniProt P0A7F3
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