Research workbench
Crystal structure of peptide-bound VASH2-svbp complex
Analyse Crystal structure of peptide-bound VASH2-svbp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JZD
- Type
- protein
- Length
- 291 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulinyl-tyr carboxypeptidase 2; Small vasohibin-binding protein; Glu-gly-glu-glu-tyr
- EC
- 3.4.17.17
- UniProt
- Q8C5G2, Q8N300
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulinyl-tyr carboxypeptidase 2 (EC 3.4.17.17) | protein | 251 | 40% helix, 20% strand | Q8C5G2 |
| B | Small vasohibin-binding protein | protein | 35 | 94% helix, 0% strand | Q8N300 |
| C | Glu-gly-glu-glu-tyr | protein | 5 | 0% helix, 0% strand | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 298 | 0.56 | 0.76 | 36 | empty |
| 2 | 109 | 0.42 | 0.76 | 21 | empty |
| 3 | 61 | 0.32 | 0.76 | 14 | empty |
| 4 | 65 | 0.26 | 0.72 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1381 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 456 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 176 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6JZD · Crystal structure of peptide-bound VASH2-SVBP complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q8C5G2 · AlphaFold monomer V2.0 prediction for tubulinyl-tyr carboxypeptidase 2 (Q8C5G2) · 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 B against A, TM-score 0.83
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 Q8C5G2
- Every structure of UniProt Q8N300
- Elsewhere: RCSB PDB 6JZD · PDBe 6JZD · UniProt Q8C5G2 · UniProt Q8N300
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