MolNFT v1 · #171188 · protein
Arabidopsis aspartate transcarbamoylase mutant F161A complex with pala
6YW9 · Pyrb: “Arabidopsis aspartate transcarbamoylase mutant F161A complex with pala”. X-ray diffraction, 1 ligand (PAL), 7 pockets (best druggability 0.78). MolNFT v1 #171188 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6YW9
- Type
- protein
- Length
- 937 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrb
- UniProt
- A0A178VJE3
- Ligands
- PAL
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrb | protein | 315 | 46% helix, 15% strand | A0A178VJE3 |
| B, C | Pyrb | protein | 311 | 47% helix, 15% strand | A0A178VJE3 |
Ligands and binding sites
- PAL · N-(phosphonacetyl)-L-aspartic acid · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · chains A
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 | 402 | 0.78 | 0.88 | 36 | empty |
| 2 | 61 | 0.72 | 0.99 | 21 | PAL |
| 3 | 62 | 0.72 | 0.98 | 23 | PAL |
| 4 | 58 | 0.71 | 0.98 | 22 | PAL |
| 5 | 65 | 0.32 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1352 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1318 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1288 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6YW9 · Arabidopsis aspartate transcarbamoylase mutant F161A 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 6YW9 · PDBe 6YW9 · UniProt A0A178VJE3
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