Research workbench
Tubulin darpin room-temperature structure in complex with colchicine determined by serial millisecond crystallography
Analyse Tubulin darpin room-temperature structure in complex with colchicine determined… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NM5
- Type
- protein
- Length
- 994 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, LOC, MG
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 422 | 46% helix, 18% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 417 | 49% helix, 19% strand | Q6B856 |
| F | Designed ankyrin repeat protein (darpin) D1 | protein | 155 | 54% helix, 0% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- LOC · N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide · ligand · chains A, B
- MG · Magnesium ion · metal · chains A, 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 | 725 | 0.85 | 0.89 | 87 | GTP, MG, LOC |
| 2 | 473 | 0.67 | 0.79 | 59 | empty |
| 3 | 199 | 0.58 | 0.81 | 34 | GDP |
| 4 | 332 | 0.58 | 0.77 | 45 | empty |
| 5 | 74 | 0.55 | 0.87 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1467 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 920 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5NM5 · Tubulin Darpin room-temperature structure in complex with Colchicine determined by serial… · 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 5NM5 · PDBe 5NM5 · UniProt P81947 · UniProt Q6B856
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