MolNFT v1 · #59762 · protein
Crystal structure of the ecdysone phosphate phosphatase, eppase, from bombix mori in complex with tungstate
3C7T · Ecdysteroid-phosphate phosphatase: “Crystal structure of the ecdysone phosphate phosphatase, eppase, from bombix mori in complex with tungstate”. X-ray diffraction, 5 ligands (NA, MG, CL), 20 pockets (best druggability 0.82). MolNFT…
- PDB
- 3C7T
- Type
- protein
- Length
- 1,036 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ecdysteroid-phosphate phosphatase
- UniProt
- Q7YTB0
- Ligands
- NA, MG, CL, IOD, WO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ecdysteroid-phosphate phosphatase | protein | 259 | 34% helix, 14% strand | Q7YTB0 |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
- MG · Magnesium ion · metal · chains C
- CL · Chloride ion · ion · 15 copies · chains A, C, B, D
- IOD · Iodide ion · ion · 6 copies · chains B, C, D
- WO4 · Tungstate(vi)ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.82 | 0.91 | 55 | WO4, CL |
| 2 | 339 | 0.77 | 0.88 | 46 | WO4, CL |
| 3 | 233 | 0.77 | 0.90 | 32 | CL, WO4 |
| 4 | 154 | 0.72 | 0.91 | 28 | CL, WO4 |
| 5 | 284 | 0.70 | 0.84 | 47 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2390 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2365 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 1097 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1063 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 146 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3C7T · Crystal structure of the ecdysone phosphate phosphatase, EPPase, from Bombix mori in… · the same entry in another collection · chain D against D, TM-score 1.00
- Q7YTB0 · AlphaFold monomer V2.0 prediction for ecdysteroid-phosphate phosphatase (Q7YTB0) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q7YTB0
- Elsewhere: RCSB PDB 3C7T · PDBe 3C7T · UniProt Q7YTB0
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