Research workbench
X-ray structure of an mtbd truncation mutant of dynein motor domain
Analyse X-ray structure of an mtbd truncation mutant of dynein motor domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VKG
- Type
- protein
- Length
- 5,807 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynein heavy chain, cytoplasmic
- UniProt
- P34036
- Ligands
- ADP, SPM, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dynein heavy chain, cytoplasmic | protein | 2954 | 58% helix, 9% strand | P34036 |
| B | Dynein heavy chain, cytoplasmic | protein | 2853 | 57% helix, 10% strand | P34036 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B
- SPM · Spermine · ligand · 4 copies · chains A, B
- MG · Magnesium ion · metal · 3 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 | 932 | 0.83 | 0.85 | 113 | ADP |
| 2 | 485 | 0.77 | 0.85 | 57 | empty |
| 3 | 370 | 0.76 | 0.87 | 47 | ADP |
| 4 | 862 | 0.76 | 0.80 | 78 | ADP |
| 5 | 1133 | 0.76 | 0.78 | 130 | empty |
Interfaces
1 interface between chains.
- A–B · 1236 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3VKG · X-ray structure of an MTBD truncation mutant of dynein motor domain · the same entry in another collection · chain B against B, 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 P34036
- Elsewhere: RCSB PDB 3VKG · PDBe 3VKG · UniProt P34036
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