Research workbench
Structure of tubulin darpin complex 1 collected by rotation serial crystallography on a coc membrane at a synchrotron source
Analyse Structure of tubulin darpin complex 1 collected by rotation serial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AC5
- Type
- protein
- Length
- 1,024 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-2B chain; Designed ankyrin repeat protein (darpin) D1
- UniProt
- P81947, Q6B856
- Ligands
- GTP, GDP, MG
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 437 | 45% helix, 17% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 431 | 48% helix, 19% strand | Q6B856 |
| F | Designed ankyrin repeat protein (darpin) D1 | protein | 156 | 52% helix, 0% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · chains A, B
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.75 | 0.84 | 69 | GTP, MG |
| 2 | 224 | 0.63 | 0.82 | 36 | GDP |
| 3 | 408 | 0.62 | 0.77 | 34 | empty |
| 4 | 142 | 0.61 | 0.85 | 25 | empty |
| 5 | 204 | 0.53 | 0.78 | 26 | PG0 |
Interfaces
2 interfaces between chains.
- A–B · 1265 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 927 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7AC5 · Structure of Tubulin Darpin complex 1 collected by rotation serial crystallography on a… · the same entry in another collection · chain A against A, 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 P81947
- Every structure of UniProt Q6B856
- Elsewhere: RCSB PDB 7AC5 · PDBe 7AC5 · UniProt P81947 · UniProt Q6B856
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