Research workbench
Crystal structure of svbp-VASH1 with peptide mimic the C-terminal of alpha-tubulin
Analyse Crystal structure of svbp-VASH1 with peptide mimic the C-terminal of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J8F
- Type
- protein
- Length
- 261 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small vasohibin-binding protein; Tubulinyl-tyr carboxypeptidase 1; 8-mer peptide
- EC
- 3.4.17.17
- UniProt
- Q8N300, Q7L8A9
- Pockets
- 1 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Small vasohibin-binding protein | protein | 22 | 91% helix, 0% strand | Q8N300 |
| B | Tubulinyl-tyr carboxypeptidase 1 (EC 3.4.17.17) | protein | 234 | 43% helix, 21% strand | Q7L8A9 |
| C | 8-mer peptide | protein | 5 | 0% helix, 0% strand | — |
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.51 | 0.78 | 27 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1059 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 503 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6J8F · Crystal structure of SVBP-VASH1 with peptide mimic the C-terminal of alpha-tubulin · 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 B against A, TM-score 0.98
- Q8N300 · AlphaFold monomer V2.0 prediction for small vasohibin-binding protein (Q8N300) · a predicted model of the same protein · chain A against A, TM-score 0.79
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 Q8N300
- Every structure of UniProt Q7L8A9
- Elsewhere: RCSB PDB 6J8F · PDBe 6J8F · UniProt Q8N300 · UniProt Q7L8A9
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