Research workbench
Oligomeric assembly of actin bound to mrtf-a
Analyse Oligomeric assembly of actin bound to mrtf-a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YJE
- Type
- protein
- Length
- 1,081 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; MKL/MYOCARDIN-like protein 1
- UniProt
- P68135, Q8K4J6
- Ligands
- LAB, ATP, MG
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin, alpha skeletal muscle | protein | 333 | 47% helix, 19% strand | P68135 |
| B | Actin, alpha skeletal muscle | protein | 351 | 47% helix, 19% strand | P68135 |
| C | Actin, alpha skeletal muscle | protein | 345 | 47% helix, 19% strand | P68135 |
| M | MKL/MYOCARDIN-like protein 1 | protein | 52 | 63% helix, 0% strand | Q8K4J6 |
Ligands and binding sites
- LAB · Latrunculin B · ligand · 3 copies · chains A, C, B
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, B, M, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.80 | 0.82 | 90 | ATP, MG, LAB |
| 2 | 1067 | 0.76 | 0.78 | 94 | empty |
| 3 | 386 | 0.73 | 0.84 | 48 | LAB, ATP, MG |
| 4 | 310 | 0.71 | 0.85 | 45 | LAB, ATP, MG |
| 5 | 216 | 0.66 | 0.85 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–M · 1012 Ų buried · 11 hydrogen bonds · protein-protein
- B–M · 940 Ų buried · 10 hydrogen bonds · protein-protein
- C–M · 666 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 351 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 180 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2YJE · Oligomeric assembly of actin bound to MRTF-A · the same entry in another collection · chain M against M, 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
- Q8K4J6 · AlphaFold monomer V2.0 prediction for myocardin-related transcription factor a (Q8K4J6) · a predicted model of the same protein · chain M against A, TM-score 0.84
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 Q8K4J6
- Elsewhere: RCSB PDB 2YJE · PDBe 2YJE · UniProt P68135 · UniProt Q8K4J6
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