MolNFT v1 · #106359 · protein
Structure of actin-lmod complex
4RWT · Actin-5C: “Structure of actin-lmod complex”. X-ray diffraction, 2 ligands (ANP, MG), 18 pockets (best druggability 0.73). MolNFT v1 #106359 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4RWT
- Type
- protein
- Length
- 1,186 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin-5C; Leiomodin-2
- UniProt
- P10987, Q6P5Q4
- Ligands
- ANP, MG
- Pockets
- 18 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Actin-5C | protein | 369 | 42% helix, 20% strand | P10987 |
| C | Leiomodin-2 | protein | 168 | 48% helix, 11% strand | Q6P5Q4 |
| D | Leiomodin-2 | protein | 280 | 40% helix, 6% strand | Q6P5Q4 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.73 | 0.79 | 60 | ANP, MG |
| 2 | 549 | 0.73 | 0.81 | 54 | empty |
| 3 | 597 | 0.72 | 0.80 | 55 | ANP, MG |
| 4 | 59 | 0.70 | 0.97 | 18 | empty |
| 5 | 328 | 0.64 | 0.79 | 46 | empty |
Interfaces
5 interfaces between chains.
- A–D · 2550 Ų buried · 30 hydrogen bonds · protein-protein
- D–B · 2223 Ų buried · 26 hydrogen bonds · protein-protein
- C–B · 1392 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 541 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 394 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4RWT · Structure of actin-Lmod complex · the same entry in another collection · chain B against B, TM-score 1.00
- Q6P5Q4 · AlphaFold monomer V2.0 prediction for leiomodin-2 (Q6P5Q4) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P10987 · AlphaFold monomer V2.0 prediction for actin-5C (P10987) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P10987
- Every structure of UniProt Q6P5Q4
- Elsewhere: RCSB PDB 4RWT · PDBe 4RWT · UniProt P10987 · UniProt Q6P5Q4
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