Research workbench
Atomic model of a microtubule seam based on a cryo-EM reconstruction of the EB3-bound microtubule (merged dataset containing tubulin bound to gtpgammas, gmpcpp, and GDP)
Analyse Atomic model of a microtubule seam based on a cryo-EM reconstruction of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JAW
- Type
- protein
- Length
- 1,722 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta chain
- UniProt
- Q2XVP4, P02554
- Ligands
- GTP, GSP, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tubulin alpha-1B chain | protein | 432 | 47% helix, 17% strand | Q2XVP4 |
| B, D | Tubulin beta chain | protein | 429 | 49% helix, 19% strand | P02554 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 2 copies · chains B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.83 | 0.94 | 49 | GSP |
| 2 | 278 | 0.82 | 0.93 | 51 | GTP, MG |
| 3 | 608 | 0.73 | 0.80 | 52 | empty |
| 4 | 551 | 0.71 | 0.80 | 45 | empty |
| 5 | 287 | 0.62 | 0.80 | 38 | GSP |
Interfaces
4 interfaces between chains.
- A–B · 1983 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1848 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 475 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 423 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3JAW · Atomic model of a microtubule seam based on a cryo-EM reconstruction of the EB3-bound… · 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 Q2XVP4
- Every structure of UniProt P02554
- Elsewhere: RCSB PDB 3JAW · PDBe 3JAW · UniProt Q2XVP4 · UniProt P02554
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