Research workbench
The crystal structure of VASH1-svbp complex
Analyse The crystal structure of VASH1-svbp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OCF
- Type
- protein
- Length
- 297 residues
- Chains
- 2
- 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
- CL
- Pockets
- 3 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulinyl-tyr carboxypeptidase 1 (EC 3.4.17.17) | protein | 248 | 39% helix, 19% strand | Q7L8A9 |
| B | Small vasohibin-binding protein | protein | 49 | 86% helix, 0% strand | Q8N300 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.43 | 0.74 | 16 | GOL |
| 2 | 63 | 0.31 | 0.75 | 15 | empty |
| 3 | 54 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1280 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 6OCF · The crystal structure of VASH1-SVBP complex · 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 0.96
- Q8N300 · AlphaFold monomer V2.0 prediction for small vasohibin-binding protein (Q8N300) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 6OCF · PDBe 6OCF · UniProt Q7L8A9 · UniProt Q8N300
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