Research workbench
Aj-gmpcpp-mt-non-seam
Analyse Aj-gmpcpp-mt-non-seam in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DN0
- Type
- protein
- Length
- 2,564 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta chain
- UniProt
- Q2XVP4, P02554
- Ligands
- GTP, G2P, TAJ, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, B, C | Tubulin alpha-1B chain | protein | 428 | 40% helix, 16% strand | Q2XVP4 |
| E, F | Tubulin beta chain | protein | 426 | 46% helix, 18% strand | P02554 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains D, A, F, B, C, E
- G2P · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains B, E, D, F
- TAJ · taccalonolide AJ · ligand · 2 copies · chains E, F
- MG · Magnesium ion · metal · 4 copies · chains D, A, F, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.84 | 0.93 | 49 | GTP, MG |
| 2 | 394 | 0.83 | 0.92 | 50 | GTP, MG |
| 3 | 352 | 0.82 | 0.92 | 49 | G2P |
| 4 | 636 | 0.81 | 0.86 | 85 | G2P |
| 5 | 589 | 0.73 | 0.81 | 59 | empty |
Interfaces
7 interfaces between chains.
- A–F · 1891 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 1848 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 1773 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 1730 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 454 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7DN0 · AJ-GMPCPP-MT-non-seam · the same entry in another collection · chain D against D, TM-score 1.00
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 Q2XVP4
- Every structure of UniProt P02554
- Elsewhere: RCSB PDB 7DN0 · PDBe 7DN0 · UniProt Q2XVP4 · UniProt P02554
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