Research workbench
Structure of human sts-1 histidine phosphatase domain with sulfate bound
Analyse Structure of human sts-1 histidine phosphatase domain with sulfate bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VR6
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-associated and SH3 domain-containing protein B
- EC
- 3.1.3.48
- UniProt
- Q8TF42
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-associated and SH3 domain-containing protein B (EC 3.1.3.48) | protein | 264 | 37% helix, 14% strand | Q8TF42 |
| B | Ubiquitin-associated and SH3 domain-containing protein B (EC 3.1.3.48) | protein | 266 | 36% helix, 14% strand | Q8TF42 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 16 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.52 | 0.86 | 19 | empty |
| 2 | 69 | 0.51 | 0.85 | 20 | empty |
| 3 | 157 | 0.44 | 0.75 | 25 | SO4 |
| 4 | 128 | 0.40 | 0.75 | 19 | empty |
| 5 | 111 | 0.39 | 0.75 | 23 | SO4 |
Interfaces
1 interface between chains.
- A–B · 2517 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 5VR6 · Structure of Human Sts-1 histidine phosphatase domain with sulfate bound · the same entry in another collection · chain A against A, TM-score 1.00
- Q8TF42 · AlphaFold monomer V2.0 prediction for ubiquitin-associated and SH3 domain-containing… · a predicted model of the same protein · chain A 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 Q8TF42
- Elsewhere: RCSB PDB 5VR6 · PDBe 5VR6 · UniProt Q8TF42
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