Research workbench
Crystal structure of the ecdysone phosphate phosphatase, eppase, from bombix mori in complex with tungstate
Analyse Crystal structure of the ecdysone phosphate phosphatase, eppase, from bombix… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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