Research workbench
Cryo-EM structure of gtpgammas-microtubule co-polymerized with EB3 (merged dataset with and without kinesin bound)
Analyse Cryo-EM structure of gtpgammas-microtubule co-polymerized with EB3 (merged… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JAK
- Type
- protein
- Length
- 5,428 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta chain; Microtubule-associated protein RP/EB family…
- UniProt
- Q2XVP4, P02554, Q9UPY8
- Ligands
- GTP, GSP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, J, C, L, A, K | Tubulin alpha-1B chain | protein | 432 | 47% helix, 17% strand | Q2XVP4 |
| F, G, D, I, B, H | Tubulin beta chain | protein | 429 | 50% helix, 20% strand | P02554 |
| N, M | Microtubule-associated protein RP/EB family member 3 | protein | 131 | 59% helix, 0% strand | Q9UPY8 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains E, G, F, J, C, I, D, L, A, H, B, K
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 6 copies · chains E, F, G, C, D, I, A, B, H
- MG · Magnesium ion · metal · 6 copies · chains E, J, C, L, A, K
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 | 373 | 0.85 | 0.94 | 56 | GSP |
| 2 | 270 | 0.84 | 0.96 | 44 | GTP, MG |
| 3 | 262 | 0.84 | 0.96 | 45 | GTP, MG |
| 4 | 527 | 0.84 | 0.90 | 77 | GSP |
| 5 | 262 | 0.84 | 0.95 | 45 | GTP, MG |
Interfaces
25 interfaces between chains.
- A–H · 1968 Ų buried · 22 hydrogen bonds · protein-protein
- B–K · 1968 Ų buried · 22 hydrogen bonds · protein-protein
- E–G · 1965 Ų buried · 22 hydrogen bonds · protein-protein
- F–J · 1965 Ų buried · 22 hydrogen bonds · protein-protein
- C–I · 1964 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3JAK · Cryo-EM structure of GTPgammaS-microtubule co-polymerized with EB3 (merged dataset with… · the same entry in another collection · chain H against H, 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
- Every structure of UniProt Q9UPY8
- Elsewhere: RCSB PDB 3JAK · PDBe 3JAK · UniProt Q2XVP4 · UniProt P02554 · UniProt Q9UPY8
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