MolNFT v1 · #157845 · protein
Crystal structure of cdp-chase: raster data collection
6NCH · Phosphohydrolase (MUTT/NUDIX family protein): “Crystal structure of cdp-chase: raster data collection”. X-ray diffraction, 3 ligands (RB5, SO4, PO4), 5 pockets (best druggability 0.67). MolNFT v1 #157845 on GenesisL1: 3D structure…
- PDB
- 6NCH
- Type
- protein
- Length
- 400 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphohydrolase (MUTT/NUDIX family protein)
- UniProt
- Q81EE8
- Ligands
- RB5, SO4, PO4
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphohydrolase (MUTT/NUDIX family protein) | protein | 204 | 36% helix, 28% strand | Q81EE8 |
| B | Phosphohydrolase (MUTT/NUDIX family protein) | protein | 196 | 32% helix, 29% strand | Q81EE8 |
Ligands and binding sites
- RB5 · D-ribose · ligand · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.67 | 0.78 | 43 | PO4, RB5 |
| 2 | 347 | 0.59 | 0.77 | 46 | empty |
| 3 | 148 | 0.45 | 0.76 | 17 | empty |
| 4 | 77 | 0.41 | 0.79 | 13 | SO4 |
| 5 | 62 | 0.27 | 0.72 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3509 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 6NCH · Crystal structure of CDP-Chase: Raster data collection · 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 Q81EE8
- Elsewhere: RCSB PDB 6NCH · PDBe 6NCH · UniProt Q81EE8
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