Research workbench
Crystal structure of unliganded aspartate transcarbamoylase from bacillus subtilis
Analyse Crystal structure of unliganded aspartate transcarbamoylase from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R7D
- Type
- protein
- Length
- 873 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate carbamoyltransferase
- EC
- 2.1.3.2
- UniProt
- P05654
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Aspartate carbamoyltransferase (EC 2.1.3.2) | protein | 291 | 45% helix, 16% strand | P05654 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 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 | 485 | 0.72 | 0.82 | 51 | PO4 |
| 2 | 440 | 0.72 | 0.82 | 50 | empty |
| 3 | 395 | 0.71 | 0.83 | 50 | PO4 |
| 4 | 406 | 0.67 | 0.80 | 43 | empty |
| 5 | 69 | 0.33 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 986 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 974 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 973 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3R7D · Crystal Structure of Unliganded Aspartate Transcarbamoylase from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- P05654 · AlphaFold monomer V2.0 prediction for aspartate carbamoyltransferase (P05654) · a predicted model of the same protein · chain A 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 P05654
- Elsewhere: RCSB PDB 3R7D · PDBe 3R7D · UniProt P05654
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