Research workbench
PROFILIN:ACTIN with a wide open nucleotide cleft
Analyse PROFILIN:ACTIN with a wide open nucleotide cleft in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UB5
- Type
- protein
- Length
- 509 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, cytoplasmic 1; Profilin-1
- UniProt
- P60712, P02584
- Ligands
- ACE, ATP, CA, CL
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin, cytoplasmic 1 | protein | 370 | 42% helix, 20% strand | P60712 |
| P | Profilin-1 | protein | 139 | 29% helix, 31% strand | P02584 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains P
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains P
- GOL · Glycerol · additive · chains P
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 | 508 | 0.71 | 0.81 | 49 | ATP, CA |
| 2 | 195 | 0.62 | 0.83 | 25 | empty |
| 3 | 149 | 0.53 | 0.80 | 33 | empty |
| 4 | 51 | 0.25 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–P · 1105 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3UB5 · Profilin:actin with a wide open nucleotide cleft · the same entry in another collection · chain A against A, TM-score 1.00
- P02584 · AlphaFold monomer V2.0 prediction for profilin-1 (P02584) · a predicted model of the same protein · chain P against A, TM-score 0.99
- P60712 · AlphaFold monomer V2.0 prediction for actin, cytoplasmic 1 (P60712) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P60712
- Every structure of UniProt P02584
- Elsewhere: RCSB PDB 3UB5 · PDBe 3UB5 · UniProt P60712 · UniProt P02584
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