Research workbench
Crystal structure of the adenylyl cyclase domain of anthrax edema factor (ef) in complex with calmodulin and 2' deoxy, 3' anthraniloyl ATP
Analyse Crystal structure of the adenylyl cyclase domain of anthrax edema factor (ef)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LVC
- Type
- protein
- Length
- 1,882 residues
- Chains
- 6
- 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, P02593
- Ligands
- DOT, CA, YB
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calmodulin-sensitive adenylate cyclase (EC 4.6.1.1) | protein | 485 | 42% helix, 16% strand | P40136 |
| B | Calmodulin-sensitive adenylate cyclase (EC 4.6.1.1) | protein | 465 | 34% helix, 16% strand | P40136 |
| C | Calmodulin-sensitive adenylate cyclase (EC 4.6.1.1) | protein | 503 | 40% helix, 16% strand | P40136 |
| D, E, F | Calmodulin | protein | 143 | 53% helix, 6% strand | P02593 |
Ligands and binding sites
- DOT · 3'anthraniloyl-2'-deoxy-adenosine-5'-triphosphate · ligand · 2 copies · chains A, C
- CA · Calcium ion · metal · 6 copies · chains D, E, F
- YB · Ytterbium (III) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.81 | 0.82 | 77 | YB, DOT |
| 2 | 885 | 0.79 | 0.82 | 76 | empty |
| 3 | 905 | 0.79 | 0.81 | 81 | DOT |
| 4 | 965 | 0.79 | 0.81 | 81 | empty |
| 5 | 1030 | 0.78 | 0.80 | 74 | empty |
Interfaces
6 interfaces between chains.
- C–F · 2944 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 2906 Ų buried · 26 hydrogen bonds · protein-protein
- B–E · 2329 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 707 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 682 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1LVC · Crystal structure of the adenylyl cyclase domain of anthrax edema factor (EF) in complex… · the same entry in another collection · chain F against F, TM-score 1.00
- P40136 · AlphaFold monomer V2.0 prediction for calmodulin-sensitive adenylate cyclase (P40136) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P02593
- Elsewhere: RCSB PDB 1LVC · PDBe 1LVC · UniProt P40136 · UniProt P02593
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