Research workbench
Crystal structure of the VASH1-svbp complex
Analyse Crystal structure of the 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
- 6NVQ
- Type
- protein
- Length
- 272 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
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Tubulinyl-tyr carboxypeptidase 1 (EC 3.4.17.17) | protein | 244 | 40% helix, 20% strand | Q7L8A9 |
| B | Small vasohibin-binding protein | protein | 28 | 86% helix, 0% strand | Q8N300 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.53 | 0.75 | 34 | empty |
| 2 | 100 | 0.47 | 0.80 | 23 | empty |
| 3 | 94 | 0.33 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- C–B · 1210 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6NVQ · Crystal structure of the VASH1-SVBP complex · the same entry in another collection · chain C against C, TM-score 1.00
- Q7L8A9 · AlphaFold monomer V2.0 prediction for tubulinyl-tyr carboxypeptidase 1 (Q7L8A9) · a predicted model of the same protein · chain C 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 B against A, TM-score 0.77
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 6NVQ · PDBe 6NVQ · UniProt Q7L8A9 · UniProt Q8N300
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