Research workbench
Cryo-EM structure of jasplakinolide-stabilized F-actin in complex with ADP
Analyse Cryo-EM structure of jasplakinolide-stabilized F-actin in complex with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OOC
- Type
- protein
- Length
- 1,855 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle
- UniProt
- P68135
- Ligands
- ADP, 9ZK, MG
- Pockets
- 13 · best druggability 0.83
Structure
electron microscopy · 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.83 | 0.84 | 117 | 9ZK |
| 2 | 820 | 0.82 | 0.84 | 97 | empty |
| 3 | 328 | 0.81 | 0.92 | 57 | ADP, MG |
| 4 | 334 | 0.80 | 0.91 | 60 | ADP, MG |
| 5 | 406 | 0.78 | 0.87 | 63 | ADP, MG |
Interfaces
7 interfaces between chains.
- C–E · 1119 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1118 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1113 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 459 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 459 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (methylation).
Compared structures
- 5OOC · Cryo-EM structure of jasplakinolide-stabilized F-actin in complex with ADP · 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 A 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 5OOC · PDBe 5OOC · UniProt P68135
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