Research workbench
Crystal structure of the 2H-phosphatase domain of sts-2
Analyse Crystal structure of the 2H-phosphatase domain of sts-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D4I
- Type
- protein
- Length
- 1,065 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sts-2 protein
- UniProt
- Q8BX41
- Ligands
- CL
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sts-2 protein | protein | 273 | 38% helix, 14% strand | Q8BX41 |
| B | Sts-2 protein | protein | 264 | 37% helix, 15% strand | Q8BX41 |
| C | Sts-2 protein | protein | 263 | 35% helix, 15% strand | Q8BX41 |
| D | Sts-2 protein | protein | 265 | 37% helix, 14% strand | Q8BX41 |
Ligands and binding sites
- CL · Chloride ion · ion · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.82 | 0.84 | 111 | empty |
| 2 | 260 | 0.70 | 0.85 | 42 | empty |
| 3 | 467 | 0.66 | 0.78 | 43 | empty |
| 4 | 425 | 0.62 | 0.76 | 43 | empty |
| 5 | 57 | 0.58 | 0.90 | 18 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2477 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 2342 Ų buried · 43 hydrogen bonds · protein-protein
- A–D · 1070 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 366 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 161 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3D4I · Crystal structure of the 2H-phosphatase domain of Sts-2 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8BX41
- Elsewhere: RCSB PDB 3D4I · PDBe 3D4I · UniProt Q8BX41
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