MolNFT v1 · #171158 · protein
Arabidopsis aspartate transcarbamoylase complex with carbamoyl phosphate
6YVB · Pyrb: “Arabidopsis aspartate transcarbamoylase complex with carbamoyl phosphate”. X-ray diffraction, 1 ligand (CP), 20 pockets (best druggability 0.84). MolNFT v1 #171158 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6YVB
- Type
- protein
- Length
- 1,889 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrb
- UniProt
- A0A178VJE3
- Ligands
- CP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Pyrb | protein | 311 | 45% helix, 15% strand | A0A178VJE3 |
| B, E | Pyrb | protein | 312 | 46% helix, 15% strand | A0A178VJE3 |
| C | Pyrb | protein | 324 | 44% helix, 15% strand | A0A178VJE3 |
| D | Pyrb | protein | 319 | 42% helix, 15% strand | A0A178VJE3 |
Ligands and binding sites
- CP · Phosphoric acid mono(formamide)ester · ligand · 6 copies · chains A, C, B, D, E, F
- GOL · Glycerol · additive · 18 copies · chains A, E, B, F, C, D
- ACT · Acetate ion · additive · 10 copies · chains A, E, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.84 | 0.85 | 106 | CP, GOL |
| 2 | 1062 | 0.82 | 0.83 | 113 | CP, ACT |
| 3 | 385 | 0.81 | 0.90 | 39 | empty |
| 4 | 350 | 0.79 | 0.90 | 37 | empty |
| 5 | 587 | 0.72 | 0.80 | 53 | CP, GOL |
Interfaces
9 interfaces between chains.
- D–E · 1240 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1145 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1135 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1121 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1111 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6YVB · Arabidopsis aspartate transcarbamoylase complex with 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 6YVB · PDBe 6YVB · UniProt A0A178VJE3
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