MolNFT v1 · #171082 · protein
Arabidopsis aspartate transcarbamoylase complex with pala and carbamoyl phosphate
6YSP · Pyrb: “Arabidopsis aspartate transcarbamoylase complex with pala and carbamoyl phosphate”. X-ray diffraction, 3 ligands (CP, PAL, SO4), 10 pockets (best druggability 0.79). MolNFT v1 #171082 on GenesisL1: 3D structure, binding sites…
- PDB
- 6YSP
- Type
- protein
- Length
- 934 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrb
- UniProt
- A0A178VJE3
- Ligands
- CP, PAL, SO4
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pyrb | protein | 311 | 47% helix, 15% strand | A0A178VJE3 |
| B | Pyrb | protein | 312 | 47% helix, 15% strand | A0A178VJE3 |
Ligands and binding sites
- CP · Phosphoric acid mono(formamide)ester · ligand · 2 copies · chains A, C, B
- PAL · N-(phosphonacetyl)-L-aspartic acid · ligand · chains B, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.79 | 0.89 | 37 | empty |
| 2 | 55 | 0.71 | 0.98 | 21 | PAL |
| 3 | 146 | 0.70 | 0.90 | 31 | empty |
| 4 | 239 | 0.70 | 0.86 | 35 | CP, SO4, GOL |
| 5 | 384 | 0.66 | 0.80 | 32 | CP |
Interfaces
3 interfaces between chains.
- B–C · 1248 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1168 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1101 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 6YSP · Arabidopsis aspartate transcarbamoylase complex with PALA and carbamoyl phosphate · 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 6YSP · PDBe 6YSP · UniProt A0A178VJE3
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