Research workbench
Structure and dynamics of single-isoform recombinant neuronal human tubulin
Analyse Structure and dynamics of single-isoform recombinant neuronal human tubulin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JCO
- Type
- protein
- Length
- 5,124 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin beta-3 chain; Tubulin alpha-1A chain
- UniProt
- Q13509, Q71U36
- Ligands
- G2P, GTP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K, I, J, C, D, L | Tubulin beta-3 chain | protein | 426 | 50% helix, 18% strand | Q13509 |
| H, E, F, A, B, G | Tubulin alpha-1A chain | protein | 428 | 48% helix, 17% strand | Q71U36 |
Ligands and binding sites
- G2P · Phosphomethylphosphonic acid guanylate ester · ligand · 6 copies · chains K, I, J, C, D, L
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains H, D, E, C, F, L, I, A, K, B, J, G
- MG · Magnesium ion · metal · 12 copies · chains K, H, D, I, E, C, J, F, L, A, B, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.85 | 0.93 | 54 | G2P, MG |
| 2 | 393 | 0.85 | 0.93 | 53 | G2P, MG |
| 3 | 658 | 0.83 | 0.88 | 95 | G2P, MG |
| 4 | 232 | 0.83 | 0.96 | 44 | GTP, MG |
| 5 | 236 | 0.83 | 0.96 | 44 | GTP, MG |
Interfaces
17 interfaces between chains.
- F–L · 1894 Ų buried · 15 hydrogen bonds · protein-protein
- I–A · 1890 Ų buried · 15 hydrogen bonds · protein-protein
- E–C · 1889 Ų buried · 15 hydrogen bonds · protein-protein
- K–B · 1887 Ų buried · 14 hydrogen bonds · protein-protein
- J–G · 1884 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5JCO · Structure and dynamics of single-isoform recombinant neuronal human tubulin · the same entry in another collection · chain G against G, 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 Q13509
- Every structure of UniProt Q71U36
- Elsewhere: RCSB PDB 5JCO · PDBe 5JCO · UniProt Q13509 · UniProt Q71U36
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