Research workbench
Crystal structure of udp-X diphosphatase
Analyse Crystal structure of udp-X diphosphatase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HFQ
- Type
- protein
- Length
- 406 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MUTT/NUDIX family protein
- UniProt
- Q97PF7
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | MUTT/NUDIX family protein | protein | 203 | 38% helix, 29% strand | Q97PF7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.74 | 0.95 | 23 | PGE |
| 2 | 502 | 0.69 | 0.80 | 48 | EDO, GOL, TRS |
| 3 | 236 | 0.55 | 0.78 | 34 | EDO, TRS, SO4 |
| 4 | 79 | 0.31 | 0.73 | 15 | EDO |
Interfaces
1 interface between chains.
- A–B · 3212 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 4HFQ · Crystal structure of UDP-X diphosphatase · 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 Q97PF7
- Elsewhere: RCSB PDB 4HFQ · PDBe 4HFQ · UniProt Q97PF7
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