Research workbench
Crystal structure of actin in complex with synthetic aplc tail analogue SF01 [(3R,4S,5R,6S,10R,11R,12R)-11-(acetyloxy)-1- (benzyloxy)-14-[FORMYL(METHYL)AMINO]-5-hydroxy-4,6,10,12-tetramethyl- 9-oxotetradecan-3-yl propanoate]
Analyse Crystal structure of actin in complex with synthetic aplc tail analogue SF01… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K42
- Type
- protein
- Length
- 1,442 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle
- UniProt
- P68135
- Ligands
- ADP, NWM, CA
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Actin, alpha skeletal muscle | protein | 360 | 43% helix, 19% strand | P68135 |
| B, C | Actin, alpha skeletal muscle | protein | 361 | 43% helix, 19% strand | P68135 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- NWM · (3R,4S,5R,6S,10R,11R,12R)-11-(acetyloxy)-1-(benzyloxy)-14-[formyl(methyl)amino]-5-hydroxy-4,6,10,12-tetramethyl-9-oxotetradecan-3-yl propanoate · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.78 | 0.80 | 120 | CA, ADP |
| 2 | 425 | 0.73 | 0.83 | 53 | CA, ADP |
| 3 | 435 | 0.73 | 0.83 | 54 | CA, ADP |
| 4 | 429 | 0.73 | 0.83 | 56 | CA, ADP |
| 5 | 194 | 0.49 | 0.76 | 27 | empty |
Interfaces
5 interfaces between chains.
- C–D · 353 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 226 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 224 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 216 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 20 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4K42 · Crystal structure of actin in complex with synthetic AplC tail analogue SF01… · the same entry in another collection · chain D against D, TM-score 1.00
- P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 4K42 · PDBe 4K42 · UniProt P68135
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