Research workbench
Crystal structure of VASH2-SVBP complex with the magic triangle I3C
Analyse Crystal structure of VASH2-SVBP complex with the magic triangle I3C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JZE
- Type
- protein
- Length
- 289 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.51
- Source
- Homo sapiens; Mus musculus
- Molecule
- Tubulinyl-Tyr carboxypeptidase 2; Small vasohibin-binding protein
- EC
- 3.4.17.17
- UniProt
- Q8C5G2, Q8N300
- Ligands
- I3C
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · resolution 2.51 · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulinyl-Tyr carboxypeptidase 2 (EC 3.4.17.17) | protein | 254 | 39% helix, 20% strand | Q8C5G2 |
| B | Small vasohibin-binding protein | protein | 35 | 89% helix, 0% strand | Q8N300 |
Ligands and binding sites
- I3C · 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid · ligand · 4 copies · chains A, B
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 | 572 | 0.67 | 0.77 | 50 | I3C |
| 2 | 75 | 0.33 | 0.74 | 16 | empty |
| 3 | 63 | 0.28 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1386 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6JZE · Crystal structure of VASH2-svbp complex with the magic triangle I3C · 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 6JZE · PDBe 6JZE · UniProt Q8C5G2 · UniProt Q8N300
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