Research workbench
Structure of a longitudinal actin dimer assembled by tandem W domains
Analyse Structure of a longitudinal actin dimer assembled by tandem W domains in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M3N
- Type
- protein
- Length
- 763 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; Neural wiskott-aldrich syndrome protein
- UniProt
- P68135, Q91YD9, P20065
- Ligands
- ATP, CA
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin, alpha skeletal muscle | protein | 364 | 41% helix, 21% strand | P68135 |
| B | Actin, alpha skeletal muscle | protein | 359 | 41% helix, 21% strand | P68135 |
| W | Neural wiskott-aldrich syndrome protein | protein | 40 | 50% helix, 5% strand | Q91YD9, P20065 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 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 | 459 | 0.75 | 0.84 | 55 | ATP, CA |
| 2 | 458 | 0.74 | 0.83 | 55 | ATP, CA |
| 3 | 369 | 0.72 | 0.83 | 38 | empty |
| 4 | 576 | 0.66 | 0.76 | 61 | empty |
| 5 | 50 | 0.25 | 0.73 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–W · 993 Ų buried · 11 hydrogen bonds · protein-protein
- B–W · 839 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 194 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified, 1 disulfide (methylation, disulfide).
Compared structures
- 3M3N · Structure of a Longitudinal Actin Dimer Assembled by Tandem W Domains · the same entry in another collection · chain B against B, TM-score 1.00
- P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q91YD9 · AlphaFold monomer V2.0 prediction for neural wiskott-aldrich syndrome protein (Q91YD9) · a predicted model of the same protein · chain W against A, TM-score 0.39
- P20065 · AlphaFold monomer V2.0 prediction for thymosin beta-4 (P20065) · a predicted model of the same protein · chain W against A, TM-score 0.32
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 Q91YD9
- Every structure of UniProt P20065
- Elsewhere: RCSB PDB 3M3N · PDBe 3M3N · UniProt P68135 · UniProt Q91YD9 · UniProt P20065
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