Research workbench
Cryoem structure of myosinvi-actin complex in the rigor (nucleotide- free) state
Analyse Cryoem structure of myosinvi-actin complex in the rigor (nucleotide- free) state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BNP
- Type
- protein
- Length
- 7,160 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unconventional myosin-VI; Actin, alpha skeletal muscle
- UniProt
- F1RQI7, P68135
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I, J, K, L, M, N | Unconventional myosin-VI | protein | 704 | 42% helix, 16% strand | F1RQI7 |
| A, B, C, D, E, F, G, H | Actin, alpha skeletal muscle | protein | 367 | 40% helix, 21% strand | P68135 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.83 | 0.87 | 79 | empty |
| 2 | 1144 | 0.83 | 0.84 | 106 | empty |
| 3 | 785 | 0.82 | 0.85 | 93 | empty |
| 4 | 519 | 0.82 | 0.88 | 62 | empty |
| 5 | 892 | 0.81 | 0.84 | 94 | empty |
Interfaces
26 interfaces between chains.
- A–C · 1193 Ų buried · 14 hydrogen bonds · protein-protein
- K–E · 1173 Ų buried · 17 hydrogen bonds · protein-protein
- E–G · 1166 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1154 Ų buried · 12 hydrogen bonds · protein-protein
- F–H · 1152 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6BNP · CryoEM structure of MyosinVI-actin complex in the rigor (nucleotide-free) state · the same entry in another collection · chain N against N, 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 F1RQI7
- Every structure of UniProt P68135
- Elsewhere: RCSB PDB 6BNP · PDBe 6BNP · UniProt F1RQI7 · UniProt P68135
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