Research workbench
Arabidopsis aspartate transcarbamoylase complex with pala
Analyse Arabidopsis aspartate transcarbamoylase complex with pala in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YS6
- Type
- protein
- Length
- 930 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrb
- UniProt
- A0A178VJE3
- Ligands
- PAL, SO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrb | protein | 313 | 44% helix, 15% strand | A0A178VJE3 |
| B | Pyrb | protein | 312 | 47% helix, 16% strand | A0A178VJE3 |
| C | Pyrb | protein | 305 | 45% helix, 16% strand | A0A178VJE3 |
Ligands and binding sites
- PAL · N-(phosphonacetyl)-L-aspartic acid · ligand · chains B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, C
- GOL · Glycerol · additive · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.78 | 0.86 | 37 | empty |
| 2 | 476 | 0.70 | 0.80 | 58 | empty |
| 3 | 55 | 0.70 | 0.98 | 23 | PAL |
| 4 | 440 | 0.67 | 0.79 | 50 | SO4, GOL |
| 5 | 105 | 0.51 | 0.82 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1266 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1110 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1093 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6YS6 · Arabidopsis aspartate transcarbamoylase complex with PALA · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A178VJE3
- Elsewhere: RCSB PDB 6YS6 · PDBe 6YS6 · UniProt A0A178VJE3
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