Research workbench
Crystal structure of VASH1-svbp complex bound with parthenolide
Analyse Crystal structure of VASH1-svbp complex bound with parthenolide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OCH
- Type
- protein
- Length
- 539 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulinyl-tyr carboxypeptidase 1; Small vasohibin-binding protein
- EC
- 3.4.17.17
- UniProt
- Q7L8A9, Q8N300
- Ligands
- M4Y, SO4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tubulinyl-tyr carboxypeptidase 1 (EC 3.4.17.17) | protein | 242 | 39% helix, 20% strand | Q7L8A9 |
| B | Small vasohibin-binding protein | protein | 28 | 89% helix, 0% strand | Q8N300 |
| D | Small vasohibin-binding protein | protein | 27 | 89% helix, 0% strand | Q8N300 |
Ligands and binding sites
- M4Y · parthenolide · ligand · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 6 copies · chains A, C
- GOL · Glycerol · additive · chains A
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 | 267 | 0.74 | 0.87 | 54 | empty |
| 2 | 216 | 0.51 | 0.76 | 26 | M4Y, SO4 |
| 3 | 90 | 0.42 | 0.78 | 24 | empty |
| 4 | 125 | 0.41 | 0.75 | 15 | M4Y |
| 5 | 100 | 0.38 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1229 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1228 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 712 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6OCH · Crystal structure of VASH1-SVBP complex bound with parthenolide · the same entry in another collection · chain A against A, TM-score 1.00
- Q7L8A9 · AlphaFold monomer V2.0 prediction for tubulinyl-tyr carboxypeptidase 1 (Q7L8A9) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q8N300 · AlphaFold monomer V2.0 prediction for small vasohibin-binding protein (Q8N300) · a predicted model of the same protein · chain D against A, TM-score 0.73
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 Q7L8A9
- Every structure of UniProt Q8N300
- Elsewhere: RCSB PDB 6OCH · PDBe 6OCH · UniProt Q7L8A9 · UniProt Q8N300
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