Research workbench
Cryo-EM structure of F-ACTIN/PLASTIN2-ABD2 complex
Analyse Cryo-EM structure of F-ACTIN/PLASTIN2-ABD2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VEC
- Type
- protein
- Length
- 6,721 residues
- Chains
- 22
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; LCP1
- UniProt
- P68135, V9HWJ7
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 2 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K | Actin, alpha skeletal muscle | protein | 370 | 43% helix, 20% strand | P68135 |
| a, b, c, d, e, f, g, h, i, j, k | LCP1 | protein | 241 | 56% helix, 0% strand | V9HWJ7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 11 copies · chains A, B, C, D, E, F, G, H, I, J, K
- MG · Magnesium ion · metal · 11 copies · chains A, B, C, D, E, F, G, H, I, J, K
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 | 380 | 0.80 | 0.89 | 55 | ADP, MG |
| 2 | 814 | 0.80 | 0.83 | 87 | empty |
| 3 | 386 | 0.79 | 0.88 | 55 | ADP, MG |
| 4 | 364 | 0.79 | 0.89 | 53 | ADP, MG |
| 5 | 407 | 0.79 | 0.88 | 59 | ADP, MG |
Interfaces
39 interfaces between chains.
- E–I · 1225 Ų buried · 13 hydrogen bonds · protein-protein
- F–J · 1218 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1215 Ų buried · 9 hydrogen bonds · protein-protein
- C–G · 1212 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 1206 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6VEC · Cryo-EM structure of F-actin/Plastin2-ABD2 complex · the same entry in another collection · chain K against K, 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 P68135
- Every structure of UniProt V9HWJ7
- Elsewhere: RCSB PDB 6VEC · PDBe 6VEC · UniProt P68135 · UniProt V9HWJ7
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