Research workbench
Crystal structure of the dynein motor domain in the amppnp-bound state
Analyse Crystal structure of the dynein motor domain in the amppnp-bound state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4W8F
- Type
- protein
- Length
- 5,217 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynein heavy chain lysozyme chimera
- EC
- 3.2.1.17
- UniProt
- P36022, P00720
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dynein heavy chain lysozyme chimera (EC 3.2.1.17) | protein | 2608 | 57% helix, 10% strand | P36022, P00720 |
| B | Dynein heavy chain lysozyme chimera (EC 3.2.1.17) | protein | 2609 | 57% helix, 10% strand | P36022, P00720 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 8 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
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 | 804 | 0.83 | 0.86 | 96 | ANP |
| 2 | 410 | 0.81 | 0.90 | 54 | ANP |
| 3 | 1032 | 0.80 | 0.81 | 109 | ANP |
| 4 | 603 | 0.77 | 0.83 | 65 | ANP |
| 5 | 1082 | 0.77 | 0.79 | 71 | empty |
Interfaces
1 interface between chains.
- A–B · 1017 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4W8F · Crystal structure of the dynein motor domain in the AMPPNP-bound state · 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 P36022
- Every structure of UniProt P00720
- Elsewhere: RCSB PDB 4W8F · PDBe 4W8F · UniProt P36022 · UniProt P00720
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