MolNFT v1 · #60922 · protein
Crystal structure of the 2H-phosphatase domain of sts-2 in complex with tungstate.
3D6A · Sts-2 protein: “Crystal structure of the 2H-phosphatase domain of sts-2 in complex with tungstate.”. X-ray diffraction, 3 ligands (MG, W, NA), 12 pockets (best druggability 0.76). MolNFT v1 #60922 on GenesisL1: 3D structure, binding…
- PDB
- 3D6A
- Type
- protein
- Length
- 1,061 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sts-2 protein
- UniProt
- Q8BX41
- Ligands
- MG, W, NA
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Sts-2 protein | protein | 266 | 38% helix, 14% strand | Q8BX41 |
| B | Sts-2 protein | protein | 264 | 33% helix, 15% strand | Q8BX41 |
| C | Sts-2 protein | protein | 265 | 32% helix, 15% strand | Q8BX41 |
Ligands and binding sites
- MG · Magnesium ion · metal · 9 copies · chains A, B, D, C
- W · Tungsten ion · metal · 4 copies · chains A, D, B, C
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.76 | 0.85 | 71 | MG, W, NA |
| 2 | 431 | 0.73 | 0.83 | 49 | W, NA |
| 3 | 252 | 0.66 | 0.83 | 37 | MG |
| 4 | 435 | 0.64 | 0.78 | 42 | empty |
| 5 | 430 | 0.63 | 0.77 | 45 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2497 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 2459 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 1100 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 432 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 182 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3D6A · Crystal structure of the 2H-phosphatase domain of Sts-2 in complex with tungstate. · 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 3D6A · PDBe 3D6A · UniProt Q8BX41
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