Research workbench
In situ structure of nebulin bound to actin filament in skeletal sarcomere
Analyse In situ structure of nebulin bound to actin filament in skeletal sarcomere in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QIM
- Type
- protein
- Length
- 2,030 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acts protein; Nebulin (mouse)
- UniProt
- A0A7K7PM04
- Ligands
- ADP, MG
- Pockets
- 19 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B, A, D, E | Acts protein | protein | 371 | 43% helix, 18% strand | A0A7K7PM04 |
| F | Nebulin (mouse) | protein | 105 | 73% helix, 0% strand | — |
| G | Nebulin (mouse) | protein | 70 | 73% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains C, B, A, D, E
- MG · Magnesium ion · metal · 5 copies · chains C, B, A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 559 | 0.85 | 0.90 | 82 | ADP, MG |
| 2 | 501 | 0.85 | 0.91 | 78 | ADP, MG |
| 3 | 577 | 0.84 | 0.89 | 76 | empty |
| 4 | 360 | 0.82 | 0.91 | 65 | ADP, MG |
| 5 | 596 | 0.82 | 0.87 | 84 | empty |
Interfaces
17 interfaces between chains.
- C–A · 1209 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 1207 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 1201 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 685 Ų buried · 3 hydrogen bonds · protein-protein
- C–F · 667 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (methylation).
Compared structures
- 7QIM · In situ structure of nebulin bound to actin filament in skeletal sarcomere · the same entry in another collection · chain C against C, TM-score 1.00
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 A0A7K7PM04
- Elsewhere: RCSB PDB 7QIM · PDBe 7QIM · UniProt A0A7K7PM04
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