MolNFT v1 · #153264 · protein
Crystal structure of svbp-VASH1 complex, mutation C169A of VASH1
6J8N · Small vasohibin-binding protein: “Crystal structure of svbp-VASH1 complex, mutation C169A of VASH1”. X-ray diffraction, 5 pockets (best druggability 0.72). MolNFT v1 #153264 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6J8N
- Type
- protein
- Length
- 518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small vasohibin-binding protein; Tubulinyl-tyr carboxypeptidase 1
- EC
- 3.4.17.17
- UniProt
- Q8N300, Q7L8A9
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Small vasohibin-binding protein | protein | 24 | 92% helix, 0% strand | Q8N300 |
| B, D | Tubulinyl-tyr carboxypeptidase 1 (EC 3.4.17.17) | protein | 235 | 42% helix, 21% strand | Q7L8A9 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.72 | 0.87 | 55 | empty |
| 2 | 174 | 0.46 | 0.75 | 25 | empty |
| 3 | 163 | 0.46 | 0.75 | 24 | empty |
| 4 | 137 | 0.44 | 0.76 | 27 | empty |
| 5 | 128 | 0.44 | 0.77 | 28 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1102 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1086 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 709 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6J8N · Crystal structure of SVBP-VASH1 complex, mutation C169A of VASH1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q7L8A9 · AlphaFold monomer V2.0 prediction for tubulinyl-tyr carboxypeptidase 1 (Q7L8A9) · 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 A against A, TM-score 0.82
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 Q8N300
- Every structure of UniProt Q7L8A9
- Elsewhere: RCSB PDB 6J8N · PDBe 6J8N · UniProt Q8N300 · UniProt Q7L8A9
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