Research workbench
Cryo-EM structure of VASH1-svbp bound to microtubules
Analyse Cryo-EM structure of VASH1-svbp bound to microtubules in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WSL
- Type
- protein
- Length
- 2,278 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1A chain; Tubulin beta-3 chain; Tubulinyl-tyr carboxypeptidase 1; Small…
- EC
- 3.4.17.17
- UniProt
- Q71U36, Q13509, Q7L8A9, Q8N300
- Ligands
- GTP, G2P
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 35% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Tubulin alpha-1A chain | protein | 431 | 32% helix, 14% strand | Q71U36 |
| B, F | Tubulin beta-3 chain | protein | 429 | 38% helix, 15% strand | Q13509 |
| C, G | Tubulinyl-tyr carboxypeptidase 1 (EC 3.4.17.17) | protein | 248 | 30% helix, 15% strand | Q7L8A9 |
| D, H | Small vasohibin-binding protein | protein | 31 | 61% helix, 0% strand | Q8N300 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, E, F
- G2P · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.84 | 0.96 | 47 | GTP |
| 2 | 237 | 0.83 | 0.96 | 41 | GTP |
| 3 | 738 | 0.74 | 0.80 | 68 | empty |
| 4 | 526 | 0.71 | 0.80 | 44 | empty |
| 5 | 944 | 0.70 | 0.75 | 71 | empty |
Interfaces
9 interfaces between chains.
- E–F · 2005 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1959 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1457 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 1433 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 608 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6WSL · Cryo-EM structure of VASH1-SVBP bound to microtubules · the same entry in another collection · chain H against H, TM-score 1.00
- Q71U36 · AlphaFold monomer V2.0 prediction for tubulin alpha-1A chain (Q71U36) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q13509 · AlphaFold monomer V2.0 prediction for tubulin beta-3 chain (Q13509) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q7L8A9 · AlphaFold monomer V2.0 prediction for tubulinyl-tyr carboxypeptidase 1 (Q7L8A9) · a predicted model of the same protein · chain C against A, TM-score 0.96
- 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 0.61
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 Q71U36
- Every structure of UniProt Q13509
- Every structure of UniProt Q7L8A9
- Every structure of UniProt Q8N300
- Elsewhere: RCSB PDB 6WSL · PDBe 6WSL · UniProt Q71U36 · UniProt Q13509 · UniProt Q7L8A9 · UniProt Q8N300
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