MolNFT v1 · #14017 · protein
Crystal structure of the adenylyl cyclase domain of anthrax edema factor (ef) in complex with calmodulin and 2' deoxy, 3' anthraniloyl ATP
1LVC · Calmodulin-sensitive adenylate cyclase: “Crystal structure of the adenylyl cyclase domain of anthrax edema factor (ef) in complex with calmodulin and…”. X-ray diffraction, 3 ligands (DOT, CA, YB), 20 pockets (best druggability…
- 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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