Research workbench
Yeast dynein motor domain in the presence of a pyrazolo-pyrimidinone- based compound, model 1
Analyse Yeast dynein motor domain in the presence of a pyrazolo-pyrimidinone- based… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MI6
- Type
- protein
- Length
- 2,419 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion protein of dynein and endolysin
- UniProt
- P36022
- Ligands
- ZG7, ATP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fusion protein of dynein and endolysin | protein | 2419 | 56% helix, 11% strand | P36022 |
Ligands and binding sites
- ZG7 · (8S)-6-(3-bromophenoxy)-2-[1-(4-chlorophenyl) cyclopropyl]-7-hydroxypyrazolo[1,5-a]pyrimidine-3-carbonitrile · ligand · 2 copies · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.85 | 0.86 | 137 | ZG7 |
| 2 | 1184 | 0.84 | 0.85 | 112 | ZG7 |
| 3 | 879 | 0.76 | 0.79 | 103 | empty |
| 4 | 1137 | 0.75 | 0.77 | 87 | empty |
| 5 | 669 | 0.73 | 0.80 | 66 | ATP, MG |
Compared structures
- 7MI6 · Yeast dynein motor domain in the presence of a pyrazolo-pyrimidi -based compound, Model 1 · 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
- Elsewhere: RCSB PDB 7MI6 · PDBe 7MI6 · UniProt P36022
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