MolNFT v1 · #182089 · protein
Structure of yeast cytoplasmic dynein with AAA3 walker B mutation bound to LIS1
7MGM · Dynein AAA3-walkerb mutant (E2488Q): “Structure of yeast cytoplasmic dynein with AAA3 walker B mutation bound to LIS1”. Electron microscopy, 3 ligands (ATP, ADP, MG), 20 pockets (best druggability 0.86). MolNFT v1 #182089 on…
- PDB
- 7MGM
- Type
- protein
- Length
- 2,964 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynein AAA3-walkerb mutant (E2488Q); Nuclear distribution protein PAC1
- UniProt
- A0A7I9C1Z7, P39946
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dynein AAA3-walkerb mutant (E2488Q) | protein | 2274 | 57% helix, 12% strand | A0A7I9C1Z7 |
| C | Nuclear distribution protein PAC1 | protein | 348 | 3% helix, 50% strand | P39946 |
| B | Nuclear distribution protein PAC1 | protein | 342 | 2% helix, 50% strand | P39946 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A
- ADP · Adenosine-5'-diphosphate · ligand · 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
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 | 1054 | 0.86 | 0.87 | 86 | empty |
| 2 | 908 | 0.84 | 0.86 | 120 | ATP |
| 3 | 932 | 0.82 | 0.84 | 84 | ADP |
| 4 | 711 | 0.82 | 0.86 | 83 | ATP, MG |
| 5 | 925 | 0.82 | 0.84 | 97 | empty |
Interfaces
3 interfaces between chains.
- A–C · 755 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 729 Ų buried · 10 hydrogen bonds · protein-protein
- C–B · 615 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7MGM · Structure of yeast cytoplasmic dynein with AAA3 Walker B mutation bound to Lis1 · the same entry in another collection · chain A against A, TM-score 1.00
- P39946 · AlphaFold monomer V2.0 prediction for nuclear distribution protein PAC1 (P39946) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 A0A7I9C1Z7
- Every structure of UniProt P39946
- Elsewhere: RCSB PDB 7MGM · PDBe 7MGM · UniProt A0A7I9C1Z7 · UniProt P39946
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