Research workbench
Hsckk (human CAMSAP1) decorated 14PF taxol-GDP microtubule
Analyse Hsckk (human CAMSAP1) decorated 14PF taxol-GDP microtubule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QVJ
- Type
- protein
- Length
- 1,834 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin-regulated spectrin-associated protein 1; Tubulin alpha-1B chain; Tubulin beta…
- UniProt
- Q5T5Y3, P68363, P07437
- Ligands
- GTP, GDP, TA1, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | Calmodulin-regulated spectrin-associated protein 1 | protein | 110 | 21% helix, 28% strand | Q5T5Y3 |
| O, X | Tubulin alpha-1B chain | protein | 432 | 36% helix, 13% strand | P68363 |
| S, U | Tubulin beta chain | protein | 430 | 40% helix, 18% strand | P07437 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains O, S, X, U
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains S, U
- TA1 · Taxol · ligand · 2 copies · chains S, U
- MG · Magnesium ion · metal · 2 copies · chains O, S, X, U
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.85 | 0.86 | 113 | GTP, MG |
| 2 | 270 | 0.83 | 0.94 | 42 | GTP, MG |
| 3 | 755 | 0.78 | 0.82 | 65 | empty |
| 4 | 739 | 0.77 | 0.81 | 53 | empty |
| 5 | 361 | 0.75 | 0.86 | 51 | empty |
Interfaces
8 interfaces between chains.
- X–U · 2065 Ų buried · 19 hydrogen bonds · protein-protein
- O–S · 2047 Ų buried · 18 hydrogen bonds · protein-protein
- I–U · 612 Ų buried · 3 hydrogen bonds · protein-protein
- I–S · 503 Ų buried · 10 hydrogen bonds · protein-protein
- O–X · 503 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6QVJ · HsCKK (human CAMSAP1) decorated 14pf taxol-GDP microtubule · the same entry in another collection · chain U against U, TM-score 1.00
- P68363 · AlphaFold monomer V2.0 prediction for tubulin alpha-1B chain (P68363) · a predicted model of the same protein · chain O against A, TM-score 0.98
- P07437 · AlphaFold monomer V2.0 prediction for tubulin beta chain (P07437) · a predicted model of the same protein · chain S against A, TM-score 0.96
- Q5T5Y3 · AlphaFold monomer V2.0 prediction for calmodulin-regulated spectrin- associated protein 1… · a predicted model of the same protein · chain I against A, TM-score 0.94
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 Q5T5Y3
- Every structure of UniProt P68363
- Every structure of UniProt P07437
- Elsewhere: RCSB PDB 6QVJ · PDBe 6QVJ · UniProt Q5T5Y3 · UniProt P68363 · UniProt P07437
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