MolNFT v1 · #110626 · protein
Crystal structure of the catalytic domain of human dual-specificity phosphatase 7 (C232S)
4Y2E · Dual specificity protein phosphatase 7: “Crystal structure of the catalytic domain of human dual-specificity phosphatase 7 (C232S)”. X-ray diffraction, 1 ligand (PO4), 4 pockets (best druggability 0.84). MolNFT v1 #110626 on…
- PDB
- 4Y2E
- Type
- protein
- Length
- 578 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dual specificity protein phosphatase 7
- EC
- 3.1.3.16, 3.1.3.48
- UniProt
- Q16829
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity protein phosphatase 7 (EC 3.1.3.16, 3.1.3.48) | protein | 146 | 44% helix, 16% strand | Q16829 |
| B | Dual specificity protein phosphatase 7 (EC 3.1.3.16, 3.1.3.48) | protein | 143 | 45% helix, 16% strand | Q16829 |
| C | Dual specificity protein phosphatase 7 (EC 3.1.3.16, 3.1.3.48) | protein | 144 | 44% helix, 16% strand | Q16829 |
| D | Dual specificity protein phosphatase 7 (EC 3.1.3.16, 3.1.3.48) | protein | 145 | 45% helix, 16% strand | Q16829 |
Ligands and binding sites
- PO4 · Phosphate 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.84 | 0.85 | 80 | empty |
| 2 | 56 | 0.36 | 0.79 | 17 | empty |
| 3 | 52 | 0.35 | 0.79 | 16 | empty |
| 4 | 50 | 0.29 | 0.76 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 635 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 634 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 541 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 523 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 53 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4Y2E · Crystal structure of the catalytic domain of human dual-specificity phosphatase 7 (C232S) · the same entry in another collection · chain D against D, TM-score 1.00
- Q16829 · AlphaFold monomer V2.0 prediction for dual specificity protein phosphatase 7 (Q16829) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q16829
- Elsewhere: RCSB PDB 4Y2E · PDBe 4Y2E · UniProt Q16829
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