Research workbench
Crystal structure of the dynamin a GTPase domain complexed with GDP, determined as myosin fusion
Analyse Crystal structure of the dynamin a GTPase domain complexed with GDP, determined… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JWY
- Type
- protein
- Length
- 1,039 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin-2 heavy CHAIN,DYNAMIN-a
- UniProt
- P08799, Q94464
- Ligands
- ADP, GDP, BGC, MG
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin-2 heavy CHAIN,DYNAMIN-a | protein | 1039 | 45% helix, 16% strand | P08799, Q94464 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.84 | 0.85 | 110 | MG, ADP |
| 2 | 110 | 0.66 | 0.90 | 22 | empty |
| 3 | 557 | 0.65 | 0.76 | 52 | empty |
| 4 | 70 | 0.55 | 0.87 | 23 | empty |
| 5 | 210 | 0.53 | 0.77 | 38 | empty |
Compared structures
- 1JWY · Crystal structure of the dynamin a GTPase domain complexed with GDP, determined as myosin… · the same entry in another collection · chain A against A, TM-score 1.00
- P08799 · AlphaFold monomer V2.0 prediction for myosin-2 heavy chain (P08799) · a predicted model of the same protein · chain A against A, TM-score 0.66
- Q94464 · AlphaFold monomer V2.0 prediction for dynamin-a (Q94464) · a predicted model of the same protein · chain A against A, TM-score 0.27
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 P08799
- Every structure of UniProt Q94464
- Elsewhere: RCSB PDB 1JWY · PDBe 1JWY · UniProt P08799 · UniProt Q94464
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