MolNFT v1 · #104524 · protein
Dcps in complex with covalent inhibitor
4QDE · M7GPPPX diphosphatase: “Dcps in complex with covalent inhibitor”. X-ray diffraction, 2 ligands (30S, PO4), 16 pockets (best druggability 0.84). MolNFT v1 #104524 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4QDE
- Type
- protein
- Length
- 1,156 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M7GPPPX diphosphatase
- EC
- 3.6.1.59
- UniProt
- Q96C86
- Ligands
- 30S, PO4
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M7GPPPX diphosphatase (EC 3.6.1.59) | protein | 287 | 31% helix, 29% strand | Q96C86 |
| B | M7GPPPX diphosphatase (EC 3.6.1.59) | protein | 288 | 32% helix, 28% strand | Q96C86 |
| C | M7GPPPX diphosphatase (EC 3.6.1.59) | protein | 289 | 32% helix, 28% strand | Q96C86 |
| D | M7GPPPX diphosphatase (EC 3.6.1.59) | protein | 292 | 32% helix, 27% strand | Q96C86 |
Ligands and binding sites
- 30S · 2-{[(2,4-diaminoquinazolin-5-yl)oxy]methyl}benzenesulfonic acid · ligand · 2 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.84 | 0.85 | 88 | PO4, 30S |
| 2 | 1112 | 0.84 | 0.85 | 87 | 30S, PO4 |
| 3 | 191 | 0.81 | 0.95 | 25 | PO4 |
| 4 | 241 | 0.79 | 0.92 | 33 | PO4 |
| 5 | 467 | 0.70 | 0.80 | 39 | empty |
Interfaces
4 interfaces between chains.
- A–B · 4758 Ų buried · 84 hydrogen bonds · protein-protein
- C–D · 4751 Ų buried · 71 hydrogen bonds · protein-protein
- B–D · 668 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 132 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
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 Q96C86
- Elsewhere: RCSB PDB 4QDE · PDBe 4QDE · UniProt Q96C86
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