Research workbench
Cryo-EM structure of flnaabd E254K bound to phalloidin-stabilized F- actin
Analyse Cryo-EM structure of flnaabd E254K bound to phalloidin-stabilized F- actin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D8C
- Type
- protein
- Length
- 2,476 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Filamin-a; Actin, alpha skeletal muscle; Phalloidin
- UniProt
- P21333, P68139
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, B, C, E | Filamin-a | protein | 121 | 60% helix, 0% strand | P21333 |
| H, J, K, L, M | Actin, alpha skeletal muscle | protein | 370 | 41% helix, 17% strand | P68139 |
| N, O, P | Phalloidin | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains H, J, K, L, M
- MG · Magnesium ion · metal · 5 copies · chains H, J, K, L, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.84 | 0.90 | 76 | empty |
| 2 | 745 | 0.81 | 0.85 | 84 | ADP, MG |
| 3 | 220 | 0.75 | 0.90 | 31 | empty |
| 4 | 185 | 0.73 | 0.90 | 24 | empty |
| 5 | 533 | 0.71 | 0.81 | 67 | ADP, MG |
Interfaces
24 interfaces between chains.
- A–J · 1441 Ų buried · 15 hydrogen bonds · protein-protein
- B–K · 1440 Ų buried · 15 hydrogen bonds · protein-protein
- D–H · 1438 Ų buried · 15 hydrogen bonds · protein-protein
- C–L · 1436 Ų buried · 15 hydrogen bonds · protein-protein
- E–M · 1434 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (nonstandard, hydroxylation).
Compared structures
- 6D8C · Cryo-EM structure of FLNaABD E254K bound to phalloidin-stabilized F-actin · the same entry in another collection · chain P against P, 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 P21333
- Every structure of UniProt P68139
- Elsewhere: RCSB PDB 6D8C · PDBe 6D8C · UniProt P21333 · UniProt P68139
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