Research workbench
Cryo-EM structure of jasplakinolide-stabilized F-actin in complex with ADP-Pi
Analyse Cryo-EM structure of jasplakinolide-stabilized F-actin in complex with ADP-Pi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OOD
- Type
- protein
- Length
- 1,855 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.7
- Source
- Oryctolagus cuniculus
- Molecule
- Actin, alpha skeletal muscle
- UniProt
- P68135
- Ligands
- ADP, 9ZK, MG, PO4
- Pockets
- 13 · best druggability 0.85
Structure
electron microscopy · resolution 3.7 · 1 distinct chain · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Actin, alpha skeletal muscle | protein | 371 | 44% helix, 20% strand | P68135 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, D, E
- 9ZK · (4~{R},7~{R},10~{S},13~{S},15~{E},19~{S})-10-(4-azanylbutyl)-4-(4-hydroxyphenyl)-7-(1~{H}-indol-3-ylmethyl)-8,13,15,19-tetramethyl-1-oxa-5,8,11-triazacyclononadec-15-ene-2,6,9,12-tetrone · ligand · 5 copies · chains A, B, C, D, E
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.85 | 0.86 | 137 | 9ZK, ADP, PO4, MG |
| 2 | 835 | 0.81 | 0.84 | 102 | empty |
| 3 | 307 | 0.80 | 0.91 | 53 | ADP, PO4, MG |
| 4 | 348 | 0.79 | 0.89 | 54 | ADP, PO4, MG |
| 5 | 346 | 0.79 | 0.89 | 55 | ADP, PO4, MG |
Interfaces
7 interfaces between chains.
- C–E · 1152 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1149 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1147 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 491 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 485 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (methylation).
Compared structures
- 5OOD · Cryo-EM structure of jasplakinolide-stabilized F-actin in complex with ADP-pi · the same entry in another collection · chain E against E, TM-score 1.00
- P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 P68135
- Elsewhere: RCSB PDB 5OOD · PDBe 5OOD · UniProt P68135
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