Research workbench
Human DCTPP1 bound to triptolide
Analyse Human DCTPP1 bound to triptolide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MU5
- Type
- protein
- Length
- 843 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dctp pyrophosphatase 1
- EC
- 3.6.1.12
- UniProt
- Q9H773
- Ligands
- TLI, MG
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dctp pyrophosphatase 1 (EC 3.6.1.12) | protein | 110 | 72% helix, 0% strand | Q9H773 |
| B | Dctp pyrophosphatase 1 (EC 3.6.1.12) | protein | 105 | 75% helix, 0% strand | Q9H773 |
| C, H | Dctp pyrophosphatase 1 (EC 3.6.1.12) | protein | 104 | 76% helix, 0% strand | Q9H773 |
| D | Dctp pyrophosphatase 1 (EC 3.6.1.12) | protein | 105 | 70% helix, 0% strand | Q9H773 |
| E | Dctp pyrophosphatase 1 (EC 3.6.1.12) | protein | 105 | 71% helix, 0% strand | Q9H773 |
| F | Dctp pyrophosphatase 1 (EC 3.6.1.12) | protein | 106 | 74% helix, 0% strand | Q9H773 |
| G | Dctp pyrophosphatase 1 (EC 3.6.1.12) | protein | 104 | 75% helix, 0% strand | Q9H773 |
Ligands and binding sites
- TLI · triptolide · ligand · 8 copies · chains A, E, G, C, B, F, H, D
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1191 | 0.77 | 0.79 | 97 | TLI |
| 2 | 139 | 0.53 | 0.81 | 21 | TLI |
| 3 | 148 | 0.53 | 0.80 | 20 | TLI |
| 4 | 82 | 0.50 | 0.84 | 15 | empty |
| 5 | 117 | 0.50 | 0.80 | 18 | TLI |
Interfaces
18 interfaces between chains.
- E–G · 3293 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 3223 Ų buried · 34 hydrogen bonds · protein-protein
- F–H · 3194 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 3156 Ų buried · 31 hydrogen bonds · protein-protein
- C–G · 774 Ų buried · 3 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 Q9H773
- Elsewhere: RCSB PDB 7MU5 · PDBe 7MU5 · UniProt Q9H773
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