MolNFT v1 · #171239 · protein
Arabidopsis aspartate transcarbamoylase in apo state
6YY1 · Pyrb: “Arabidopsis aspartate transcarbamoylase in apo state”. X-ray diffraction, 20 pockets (best druggability 0.80). MolNFT v1 #171239 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6YY1
- Type
- protein
- Length
- 1,843 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrb
- UniProt
- A0A178VJE3
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrb | protein | 305 | 44% helix, 15% strand | A0A178VJE3 |
| B | Pyrb | protein | 304 | 44% helix, 16% strand | A0A178VJE3 |
| C, F | Pyrb | protein | 304 | 45% helix, 16% strand | A0A178VJE3 |
| D | Pyrb | protein | 312 | 43% helix, 16% strand | A0A178VJE3 |
| E | Pyrb | protein | 314 | 43% helix, 15% strand | A0A178VJE3 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.80 | 0.88 | 38 | empty |
| 2 | 392 | 0.79 | 0.88 | 39 | empty |
| 3 | 661 | 0.79 | 0.84 | 75 | empty |
| 4 | 732 | 0.76 | 0.81 | 83 | empty |
| 5 | 425 | 0.72 | 0.83 | 57 | empty |
Interfaces
9 interfaces between chains.
- A–C · 1095 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 1032 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 1020 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1011 Ų buried · 21 hydrogen bonds · protein-protein
- C–F · 1003 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6YY1 · Arabidopsis aspartate transcarbamoylase in apo state · 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 6YY1 · PDBe 6YY1 · UniProt A0A178VJE3
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