Research workbench
The structure of the aspartate transcarbamoylase trimer from staphylococcus aureus complexed with pala at 2.27 resolution.
Analyse The structure of the aspartate transcarbamoylase trimer from staphylococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PNZ
- Type
- protein
- Length
- 879 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate carbamoyltransferase
- EC
- 2.1.3.2
- UniProt
- Q5HGN2
- Ligands
- PAL
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Aspartate carbamoyltransferase (EC 2.1.3.2) | protein | 293 | 46% helix, 15% strand | Q5HGN2 |
Ligands and binding sites
- PAL · N-(phosphonacetyl)-L-aspartic acid · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.78 | 0.87 | 46 | empty |
| 2 | 67 | 0.74 | 0.99 | 24 | PAL |
| 3 | 64 | 0.73 | 0.98 | 22 | PAL |
| 4 | 55 | 0.70 | 0.98 | 20 | PAL |
| 5 | 76 | 0.44 | 0.81 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1183 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1167 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1152 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6PNZ · The structure of the Aspartate Transcarbamoylase trimer from Staphylococcus aureus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5HGN2 · AlphaFold monomer V2.0 prediction for aspartate carbamoyltransferase (Q5HGN2) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q5HGN2
- Elsewhere: RCSB PDB 6PNZ · PDBe 6PNZ · UniProt Q5HGN2
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