MolNFT v1 · #157846 · protein
Crystal structure of cdp-chase: vector data collection
6NCI · Phosphohydrolase (MUTT/NUDIX family protein): “Crystal structure of cdp-chase: vector data collection”. X-ray diffraction, 3 ligands (RB5, SO4, PO4), 5 pockets (best druggability 0.68). MolNFT v1 #157846 on GenesisL1: 3D structure…
- PDB
- 6NCI
- Type
- protein
- Length
- 401 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 0.68
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 28% 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 | 197 | 31% helix, 28% strand | Q81EE8 |
Ligands and binding sites
- RB5 · D-ribose · ligand · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.68 | 0.78 | 42 | PO4, RB5 |
| 2 | 420 | 0.64 | 0.78 | 52 | empty |
| 3 | 258 | 0.52 | 0.75 | 29 | SO4 |
| 4 | 50 | 0.36 | 0.80 | 18 | empty |
| 5 | 54 | 0.26 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3398 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 6NCI · Crystal structure of CDP-Chase: Vector 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 6NCI · PDBe 6NCI · UniProt Q81EE8
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