Research workbench
Crystal structure of vash 2 in complex with svbp
Analyse Crystal structure of vash 2 in complex with svbp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QBY
- Type
- protein
- Length
- 548 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
- Q86V25, Q8N300
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulinyl-tyr carboxypeptidase 2 (EC 3.4.17.17) | protein | 245 | 38% helix, 21% strand | Q86V25 |
| B | Small vasohibin-binding protein | protein | 28 | 93% helix, 0% strand | Q8N300 |
| C | Tubulinyl-tyr carboxypeptidase 2 (EC 3.4.17.17) | protein | 245 | 38% helix, 20% strand | Q86V25 |
| D | Small vasohibin-binding protein | protein | 30 | 90% helix, 0% strand | Q8N300 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.61 | 0.76 | 41 | empty |
| 2 | 361 | 0.61 | 0.77 | 38 | empty |
| 3 | 216 | 0.53 | 0.77 | 23 | empty |
| 4 | 59 | 0.38 | 0.79 | 16 | empty |
| 5 | 67 | 0.29 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1322 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1232 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 427 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6QBY · Crystal structure of VASH 2 in complex with SVBP · the same entry in another collection · chain D against D, TM-score 1.00
- Q86V25 · AlphaFold monomer V2.0 prediction for tubulinyl-tyr carboxypeptidase 2 (Q86V25) · a predicted model of the same protein · chain C 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 0.84
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 6QBY · PDBe 6QBY · UniProt Q86V25 · UniProt Q8N300
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