MolNFT v1 · #28007 · protein
Crystal structure of anthrax edema factor (ef) in complex with calmodulin and pyrophosphate
1Y0V · Calmodulin-sensitive adenylate cyclase: “Crystal structure of anthrax edema factor (ef) in complex with calmodulin and pyrophosphate”. X-ray diffraction, 3 ligands (POP, CA, MG), 20 pockets (best druggability 0.75). MolNFT v1 #28007…
- PDB
- 1Y0V
- Type
- protein
- Length
- 5,286 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin-sensitive adenylate cyclase; Calmodulin
- EC
- 4.6.1.1
- UniProt
- P40136, P62155
- Ligands
- POP, CA, MG
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Calmodulin-sensitive adenylate cyclase (EC 4.6.1.1) | protein | 735 | 38% helix, 12% strand | P40136 |
| H, I, J, K, L, M | Calmodulin | protein | 146 | 42% helix, 4% strand | P62155 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 6 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 18 copies · chains H, I, J, K, L, M
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
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 | 386 | 0.75 | 0.85 | 53 | empty |
| 2 | 368 | 0.74 | 0.85 | 50 | empty |
| 3 | 401 | 0.74 | 0.84 | 50 | empty |
| 4 | 371 | 0.74 | 0.85 | 46 | empty |
| 5 | 379 | 0.74 | 0.84 | 43 | empty |
Interfaces
12 interfaces between chains.
- F–M · 3006 Ų buried · 20 hydrogen bonds · protein-protein
- A–H · 3003 Ų buried · 20 hydrogen bonds · protein-protein
- D–K · 2997 Ų buried · 20 hydrogen bonds · protein-protein
- C–J · 2993 Ų buried · 21 hydrogen bonds · protein-protein
- E–L · 2992 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1Y0V · Crystal structure of anthrax edema factor (EF) in complex with calmodulin and… · the same entry in another collection · chain M against M, 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 P40136
- Every structure of UniProt P62155
- Elsewhere: RCSB PDB 1Y0V · PDBe 1Y0V · UniProt P40136 · UniProt P62155
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