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
- 6J4V
- Type
- protein
- Length
- 287 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulinyl-tyr carboxypeptidase 2; Small vasohibin-binding protein; Tubulin alpha-1B chain
- EC
- 3.4.17.17
- UniProt
- Q86V25, Q8N300, P68363
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 3 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 | 246 | 39% helix, 21% strand | Q86V25 |
| B | Small vasohibin-binding protein | protein | 36 | 92% helix, 0% strand | Q8N300 |
| C | Tubulin alpha-1B chain | protein | 5 | 0% helix, 0% strand | P68363 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 230 | 0.51 | 0.75 | 24 | empty |
| 2 | 57 | 0.45 | 0.83 | 17 | empty |
| 3 | 56 | 0.38 | 0.80 | 14 | empty |
| 4 | 62 | 0.30 | 0.75 | 14 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 1400 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 521 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6J4V · 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 0.76
- P68363 · AlphaFold monomer V2.0 prediction for tubulin alpha-1B chain (P68363) · a predicted model of the same protein · chain C against A, TM-score 0.55
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
- Every structure of UniProt P68363
- Elsewhere: RCSB PDB 6J4V · PDBe 6J4V · UniProt Q86V25 · UniProt Q8N300 · UniProt P68363
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