Research workbench
Cryo-EM structure of the mamk filament at 6.5 a
Analyse Cryo-EM structure of the mamk filament at 6.5 a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JYG
- Type
- protein
- Length
- 4,592 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin-like ATPase
- UniProt
- Q2W8Q6
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N | Actin-like ATPase | protein | 328 | 34% helix, 20% strand | Q2W8Q6 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
- MG · Magnesium ion · metal · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
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 | 911 | 0.86 | 0.88 | 113 | MG, ADP |
| 2 | 1044 | 0.85 | 0.85 | 101 | MG, ADP |
| 3 | 1057 | 0.84 | 0.85 | 112 | MG, ADP |
| 4 | 1200 | 0.84 | 0.85 | 127 | MG, ADP |
| 5 | 1103 | 0.83 | 0.84 | 114 | MG, ADP |
Interfaces
19 interfaces between chains.
- A–H · 716 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 691 Ų buried · 6 hydrogen bonds · protein-protein
- I–J · 690 Ų buried · 6 hydrogen bonds · protein-protein
- G–N · 689 Ų buried · 6 hydrogen bonds · protein-protein
- M–N · 689 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5JYG · Cryo-EM structure of the MamK filament at 6.5 A · 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 Q2W8Q6
- Elsewhere: RCSB PDB 5JYG · PDBe 5JYG · UniProt Q2W8Q6
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