Research workbench
Structural basis of tubulin detyrosination
Analyse Structural basis of tubulin detyrosination in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JZC
- Type
- protein
- Length
- 572 residues
- Chains
- 4
- 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
- Q8C5G2, Q8N300
- Pockets
- 11 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulinyl-tyr carboxypeptidase 2 (EC 3.4.17.17) | protein | 251 | 39% helix, 20% strand | Q8C5G2 |
| B | Tubulinyl-tyr carboxypeptidase 2 (EC 3.4.17.17) | protein | 253 | 38% helix, 19% strand | Q8C5G2 |
| C | Small vasohibin-binding protein | protein | 35 | 94% helix, 0% strand | Q8N300 |
| D | Small vasohibin-binding protein | protein | 33 | 94% helix, 0% strand | Q8N300 |
Ligands and binding sites
- GOL · Glycerol · additive · 8 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.63 | 0.77 | 52 | empty |
| 2 | 417 | 0.62 | 0.76 | 48 | empty |
| 3 | 56 | 0.43 | 0.83 | 17 | empty |
| 4 | 52 | 0.43 | 0.83 | 17 | empty |
| 5 | 74 | 0.39 | 0.78 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1370 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1364 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 341 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6JZC · Structural basis of tubulin detyrosination · the same entry in another collection · chain D against D, TM-score 1.00
- Q8C5G2 · AlphaFold monomer V2.0 prediction for tubulinyl-tyr carboxypeptidase 2 (Q8C5G2) · a predicted model of the same protein · chain B 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 D against A, TM-score 0.85
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 6JZC · PDBe 6JZC · UniProt Q8C5G2 · UniProt Q8N300
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