MolNFT v1 · #153139 · protein
Structural basis of tubulin detyrosination by vasohibins-svbp enzyme complex and functional implications
6J4Q · Tubulinyl-tyr carboxypeptidase 2: “Structural basis of tubulin detyrosination by vasohibins-svbp enzyme complex and functional implications”. X-ray diffraction, 1 ligand (TQ8), 15 pockets (best druggability 0.78). MolNFT v1 #153139…
- PDB
- 6J4Q
- Type
- protein
- Length
- 1,113 residues
- Chains
- 8
- 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
- TQ8
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 7 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, J | Tubulinyl-tyr carboxypeptidase 2 (EC 3.4.17.17) | protein | 247 | 38% helix, 21% strand | Q86V25 |
| B | Small vasohibin-binding protein | protein | 33 | 91% helix, 0% strand | Q8N300 |
| C | Tubulinyl-tyr carboxypeptidase 2 (EC 3.4.17.17) | protein | 245 | 41% helix, 20% strand | Q86V25 |
| D | Small vasohibin-binding protein | protein | 34 | 88% helix, 0% strand | Q8N300 |
| F | Tubulinyl-tyr carboxypeptidase 2 (EC 3.4.17.17) | protein | 246 | 39% helix, 21% strand | Q86V25 |
| G | Small vasohibin-binding protein | protein | 32 | 81% helix, 0% strand | Q8N300 |
| K | Small vasohibin-binding protein | protein | 29 | 90% helix, 0% strand | Q8N300 |
Ligands and binding sites
- TQ8 · N-[(2S)-4-chloro-3-oxo-1-phenyl-butan-2-yl]-4-methyl-benzenesulfonamide · ligand · 6 copies · chains A, B, C, F, G, J
- GOL · Glycerol · additive · 5 copies · chains A, F, C, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.78 | 0.81 | 83 | TQ8, GOL |
| 2 | 733 | 0.75 | 0.80 | 72 | empty |
| 3 | 258 | 0.60 | 0.79 | 30 | TQ8, GOL |
| 4 | 419 | 0.60 | 0.75 | 47 | TQ8, GOL |
| 5 | 253 | 0.56 | 0.77 | 31 | TQ8, GOL |
Interfaces
12 interfaces between chains.
- C–D · 1333 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1326 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 1316 Ų buried · 11 hydrogen bonds · protein-protein
- J–K · 1256 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 923 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 6J4Q · Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and… · the same entry in another collection · chain K against K, 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 D against A, TM-score 0.86
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 6J4Q · PDBe 6J4Q · UniProt Q86V25 · UniProt Q8N300
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