MolNFT v1 · #51351 · protein
Structure of mal-RPEL1 complexed to actin
2V51 · Actin, alpha skeletal muscle: “Structure of mal-RPEL1 complexed to actin”. X-ray diffraction, 4 ligands (ATP, LAB, CA), 3 pockets (best druggability 0.76). MolNFT v1 #51351 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2V51
- Type
- protein
- Length
- 759 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
- ATP, LAB, CA, SCN
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Actin, alpha skeletal muscle | protein | 351 | 45% helix, 20% strand | P68135 |
| D | Actin, alpha skeletal muscle | protein | 352 | 43% helix, 20% strand | P68135 |
| E, F | MKL/MYOCARDIN-like protein 1 | protein | 28 | 54% helix, 0% strand | Q8K4J6 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains B, D
- LAB · Latrunculin B · ligand · 2 copies · chains B, D
- CA · Calcium ion · metal · 2 copies · chains B, D
- SCN · Thiocyanate ion · ion · 4 copies · chains B, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.76 | 0.78 | 84 | empty |
| 2 | 371 | 0.75 | 0.86 | 51 | ATP, CA, LAB |
| 3 | 362 | 0.75 | 0.86 | 48 | ATP, CA, LAB |
Interfaces
4 interfaces between chains.
- B–F · 844 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 844 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 449 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 354 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2V51 · Structure of MAL-RPEL1 complexed to actin · 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 0.99
- Q8K4J6 · AlphaFold monomer V2.0 prediction for myocardin-related transcription factor a (Q8K4J6) · a predicted model of the same protein · chain E against A, TM-score 0.77
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 2V51 · PDBe 2V51 · UniProt P68135 · UniProt Q8K4J6
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