Research workbench
Ternary complex of profilin-actin with the poly-pro-gab domain of vasp*
Analyse Ternary complex of profilin-actin with the poly-pro-gab domain of vasp* in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PBD
- Type
- protein
- Length
- 527 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; Profilin-1; Vasodilator-stimulated phosphoprotein
- UniProt
- P68135, P07737, P50552
- Ligands
- ATP, CA
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin, alpha skeletal muscle | protein | 360 | 46% helix, 20% strand | P68135 |
| P | Profilin-1 | protein | 139 | 29% helix, 32% strand | P07737 |
| V | Vasodilator-stimulated phosphoprotein | protein | 28 | 21% helix, 4% strand | P50552 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.74 | 0.84 | 53 | CA, ATP |
| 2 | 313 | 0.64 | 0.80 | 50 | empty |
| 3 | 165 | 0.58 | 0.82 | 29 | empty |
| 4 | 73 | 0.31 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–P · 1176 Ų buried · 20 hydrogen bonds · protein-protein
- A–V · 590 Ų buried · 4 hydrogen bonds · protein-protein
- P–V · 512 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 2PBD · Ternary complex of profilin-actin with the poly-PRO-GAB domain of VASP* · 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 0.97
- P07737 · AlphaFold monomer V2.0 prediction for profilin-1 (P07737) · a predicted model of the same protein · chain P against A, TM-score 0.97
- P50552 · AlphaFold monomer V2.0 prediction for vasodilator-stimulated phosphoprotein (P50552) · a predicted model of the same protein · chain V against A, TM-score 0.30
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
- Every structure of UniProt P07737
- Every structure of UniProt P50552
- Elsewhere: RCSB PDB 2PBD · PDBe 2PBD · UniProt P68135 · UniProt P07737 · UniProt P50552
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