Research workbench
Structural basis of tubulin detyrosination by vasohibins-svbp enzyme complex and functional implications
Analyse Structural basis of tubulin detyrosination by vasohibins-svbp enzyme complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J4P
- Type
- protein
- Length
- 290 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulinyl-tyr carboxypeptidase 2; Small vasohibin-binding protein
- EC
- 3.4.17.17
- UniProt
- Q86V25, Q8N300
- Ligands
- BJL
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulinyl-tyr carboxypeptidase 2 (EC 3.4.17.17) | protein | 246 | 40% helix, 21% strand | Q86V25 |
| B | Small vasohibin-binding protein | protein | 44 | 86% helix, 0% strand | Q8N300 |
Ligands and binding sites
- BJL · N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-tyrosine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.68 | 0.79 | 51 | BJL |
| 2 | 63 | 0.40 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1368 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6J4P · Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q86V25 · AlphaFold monomer V2.0 prediction for tubulinyl-tyr carboxypeptidase 2 (Q86V25) · 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 0.79
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 Q86V25
- Every structure of UniProt Q8N300
- Elsewhere: RCSB PDB 6J4P · PDBe 6J4P · UniProt Q86V25 · UniProt Q8N300
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