Research workbench
Rabbit-muscle G-actin in complex with myxobacterial rhizopodin
Analyse Rabbit-muscle G-actin in complex with myxobacterial rhizopodin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VYP
- Type
- protein
- Length
- 687 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle
- UniProt
- P68135
- Ligands
- ATP, RH9, CA
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin, alpha skeletal muscle | protein | 358 | 44% helix, 20% strand | P68135 |
| B | Actin, alpha skeletal muscle | protein | 329 | 46% helix, 19% strand | P68135 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- RH9 · Rhizopodin · ligand · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- HEZ · Hexane-1,6-diol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.75 | 0.86 | 55 | ATP, CA |
| 2 | 272 | 0.71 | 0.86 | 42 | ATP, CA |
| 3 | 467 | 0.57 | 0.73 | 49 | HEZ |
| 4 | 158 | 0.53 | 0.79 | 33 | empty |
| 5 | 156 | 0.47 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 203 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2VYP · Rabbit-muscle G-actin in complex with myxobacterial rhizopodin · 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 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 P68135
- Elsewhere: RCSB PDB 2VYP · PDBe 2VYP · UniProt P68135
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