Research workbench
Mouse dctpase in complex with 5-me-dcmp
Analyse Mouse dctpase in complex with 5-me-dcmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SQW
- Type
- protein
- Length
- 226 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dctp pyrophosphatase 1
- EC
- 3.6.1.12
- UniProt
- Q9QY93
- Ligands
- 5CM, MG
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dctp pyrophosphatase 1 (EC 3.6.1.12) | protein | 114 | 71% helix, 0% strand | Q9QY93 |
| D | Dctp pyrophosphatase 1 (EC 3.6.1.12) | protein | 112 | 70% helix, 0% strand | Q9QY93 |
Ligands and binding sites
- 5CM · 5-methyl-2'-deoxy-cytidine-5'-monophosphate · ligand · 2 copies · chains A, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.38 | 0.79 | 13 | empty |
| 2 | 63 | 0.36 | 0.78 | 11 | empty |
Interfaces
1 interface between chains.
- A–D · 755 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 Q9QY93
- Elsewhere: RCSB PDB 6SQW · PDBe 6SQW · UniProt Q9QY93
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