Research workbench
Revised model of leiomodin 2-mediated actin regulation (alternate refinement of pdb 4RWT)
Analyse Revised model of leiomodin 2-mediated actin regulation (alternate refinement of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WFN
- Type
- protein
- Length
- 1,126 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
- 11 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Actin-5C | protein | 370 | 42% helix, 20% strand | P10987 |
| C, D | Leiomodin-2 | protein | 193 | 51% helix, 8% 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
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 788 | 0.73 | 0.78 | 73 | empty |
| 2 | 528 | 0.73 | 0.81 | 54 | ANP, MG |
| 3 | 515 | 0.72 | 0.81 | 54 | ANP, MG |
| 4 | 159 | 0.67 | 0.87 | 30 | empty |
| 5 | 247 | 0.63 | 0.81 | 39 | empty |
Interfaces
4 interfaces between chains.
- A–C · 2302 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 2279 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 568 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 50 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5WFN · Revised model of leiomodin 2-mediated actin regulation (alternate refinement of PDB 4RWT) · the same entry in another collection · chain A against A, TM-score 1.00
- P10987 · AlphaFold monomer V2.0 prediction for actin-5C (P10987) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q6P5Q4 · AlphaFold monomer V2.0 prediction for leiomodin-2 (Q6P5Q4) · a predicted model of the same protein · chain C against A, TM-score 0.87
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 5WFN · PDBe 5WFN · UniProt P10987 · UniProt Q6P5Q4
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