Research workbench
Crystal structure of a ybjq-like protein of unknown function (SSO2532) from sulfolobus solfataricus P2 at 1.76 a resolution
Analyse Crystal structure of a ybjq-like protein of unknown function (SSO2532) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VPH
- Type
- protein
- Length
- 838 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein SSO2532
- UniProt
- Q97VS8
- Ligands
- K, PO4, CL
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Hypothetical protein SSO2532 | protein | 138 | 29% helix, 40% strand | Q97VS8 |
| B | Hypothetical protein SSO2532 | protein | 137 | 29% helix, 40% strand | Q97VS8 |
| C | Hypothetical protein SSO2532 | protein | 144 | 28% helix, 38% strand | Q97VS8 |
| F | Hypothetical protein SSO2532 | protein | 143 | 28% helix, 38% strand | Q97VS8 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 11 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · chains C
- EDO · 1,2-ethanediol · additive · chains A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.77 | 0.79 | 72 | empty |
| 2 | 55 | 0.69 | 0.98 | 18 | empty |
| 3 | 52 | 0.68 | 0.98 | 17 | empty |
| 4 | 102 | 0.37 | 0.75 | 18 | EDO |
Interfaces
12 interfaces between chains.
- D–F · 1487 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1472 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1467 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1454 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1441 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 1VPH · CRYSTAL STRUCTURE OF a YbjQ-like protein of unknown function (SSO2532) FROM SULFOLOBUS… · 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 Q97VS8
- Elsewhere: RCSB PDB 1VPH · PDBe 1VPH · UniProt Q97VS8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.