MolNFT v1 · #187454 · protein
Crystal structure of vaccinia virus decapping enzyme D9 in complex with M7GDP
7SEZ · DNA repair ntp-phosphohydrolase: “Crystal structure of vaccinia virus decapping enzyme D9 in complex with M7GDP”. X-ray diffraction, 2 ligands (8NK, NA), 3 pockets (best druggability 0.68). MolNFT v1 #187454 on GenesisL1: 3D…
- PDB
- 7SEZ
- Type
- protein
- Length
- 210 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair ntp-phosphohydrolase
- UniProt
- L7QJE0
- Ligands
- 8NK, NA
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair ntp-phosphohydrolase | protein | 210 | 25% helix, 31% strand | L7QJE0 |
Ligands and binding sites
- 8NK · 7-methylguanosine 5'-diphosphate · ligand · chains A
- NA · Sodium ion · metal · 9 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.68 | 0.83 | 32 | 8NK, NA |
| 2 | 55 | 0.35 | 0.79 | 17 | NA |
| 3 | 67 | 0.30 | 0.74 | 17 | NA |
Compared structures
- 7SEZ · Crystal structure of Vaccinia Virus decapping enzyme D9 in complex with m7GDP · 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 L7QJE0
- Elsewhere: RCSB PDB 7SEZ · PDBe 7SEZ · UniProt L7QJE0
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