Research workbench
Cryo-EM structure of F-actin in complex with appnhp (amppnp)
Analyse Cryo-EM structure of F-actin in complex with appnhp (amppnp) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OOE
- Type
- protein
- Length
- 1,810 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle
- UniProt
- P68135
- Ligands
- ANP, MG
- Pockets
- 15 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Actin, alpha skeletal muscle | protein | 362 | 44% helix, 20% strand | P68135 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 5 copies · chains A, B, C, D, E
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 963 | 0.82 | 0.83 | 98 | empty |
| 2 | 329 | 0.80 | 0.91 | 58 | ANP, MG |
| 3 | 304 | 0.80 | 0.91 | 51 | ANP, MG |
| 4 | 301 | 0.79 | 0.91 | 50 | ANP, MG |
| 5 | 282 | 0.79 | 0.91 | 48 | ANP, MG |
Interfaces
7 interfaces between chains.
- B–D · 928 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 926 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 922 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 425 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 425 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (methylation).
Compared structures
- 5OOE · Cryo-EM structure of F-actin in complex with AppNHp (AMPPNP) · the same entry in another collection · chain E against E, 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 0.96
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
- Elsewhere: RCSB PDB 5OOE · PDBe 5OOE · UniProt P68135
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.