Research workbench
Microtubule binding domain from mouse cytoplasmic dynein as a fusion with seryl-tRNA synthetase
Analyse Microtubule binding domain from mouse cytoplasmic dynein as a fusion with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ERR
- Type
- protein
- Length
- 1,054 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.27
- Source
- Mus musculus; Thermus thermophilus
- Molecule
- fusion protein of microtubule binding domain from mouse cytoplasmic dynein and seryl-tRNA…
- UniProt
- Q9JHU4, P34945
- Ligands
- AMP
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.27 · 1 distinct chain · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | fusion protein of microtubule binding domain from mouse cytoplasmic dynein and seryl-tRNA synthetase from Thermus thermophilus | protein | 527 | 50% helix, 17% strand | Q9JHU4, P34945 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 636 | 0.76 | 0.82 | 66 | AMP |
| 2 | 627 | 0.75 | 0.81 | 68 | AMP |
| 3 | 267 | 0.58 | 0.78 | 25 | empty |
| 4 | 227 | 0.55 | 0.78 | 22 | empty |
| 5 | 102 | 0.53 | 0.83 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2272 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3ERR · Microtubule binding domain from mouse cytoplasmic dynein as a fusion with seryl-tRNA… · the same entry in another collection · chain A against A, TM-score 1.00
- P34945 · AlphaFold monomer V2.0 prediction for serine--tRNA ligase (P34945) · a predicted model of the same protein · chain A against A, TM-score 0.73
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 Q9JHU4
- Every structure of UniProt P34945
- Elsewhere: RCSB PDB 3ERR · PDBe 3ERR · UniProt Q9JHU4 · UniProt P34945
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