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Crystal structure of an actin monomer in complex with the nucleator Cordon-Bleu MET72NLE WH2-motif peptide
Analyse Crystal structure of an actin monomer in complex with the nucleator Cordon-Bleu… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YPU
- Type
- protein
- Length
- 749 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Oryctolagus cuniculus; SYNTHETIC CONSTRUCT
- Molecule
- Actin, alpha skeletal muscle; Cordon-Bleu WH2 motif
- UniProt
- P68135
- Ligands
- ATP, CA
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · resolution 2 · 3 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin, alpha skeletal muscle | protein | 352 | 46% helix, 19% strand | P68135 |
| B, D | Cordon-Bleu WH2 motif | protein | 22 | 64% helix, 5% strand | — |
| C | Actin, alpha skeletal muscle | protein | 353 | 45% helix, 19% strand | P68135 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, C
- CA · Calcium ion · metal · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.75 | 0.87 | 48 | ATP, CA |
| 2 | 331 | 0.74 | 0.86 | 46 | ATP, CA |
| 3 | 263 | 0.54 | 0.76 | 34 | empty |
| 4 | 245 | 0.53 | 0.76 | 32 | empty |
| 5 | 225 | 0.52 | 0.77 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 880 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 837 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 411 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5YPU · Crystal structure of an actin monomer in complex with the nucleator cordon-bleu MET72NLE… · the same entry in another collection · chain A against A, 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 0.99
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 5YPU · PDBe 5YPU · UniProt P68135
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