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Crystal structure of the adenylyl cyclase domain of anthrax edema factor (ef) in complex with calmodulin and 3' deoxy-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
- 1K90
- 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
- 3AT, CA, YB
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calmodulin-sensitive adenylate cyclase (EC 4.6.1.1) | protein | 485 | 39% helix, 15% strand | P40136 |
| D, E, F | Calmodulin | protein | 143 | 53% helix, 3% strand | P02593 |
| B | Calmodulin-sensitive adenylate cyclase (EC 4.6.1.1) | protein | 465 | 37% helix, 16% strand | P40136 |
| C | Calmodulin-sensitive adenylate cyclase (EC 4.6.1.1) | protein | 503 | 38% helix, 16% strand | P40136 |
Ligands and binding sites
- 3AT · 3'-deoxyadenosine-5'-triphosphate · ligand · 3 copies · chains A, B, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.80 | 0.82 | 78 | YB, 3AT |
| 2 | 978 | 0.80 | 0.81 | 91 | empty |
| 3 | 927 | 0.80 | 0.82 | 82 | 3AT |
| 4 | 853 | 0.78 | 0.82 | 87 | empty |
| 5 | 1162 | 0.78 | 0.80 | 84 | 3AT |
Interfaces
6 interfaces between chains.
- A–D · 2918 Ų buried · 35 hydrogen bonds · protein-protein
- C–F · 2891 Ų buried · 32 hydrogen bonds · protein-protein
- B–E · 2213 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 706 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 685 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1K90 · 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 0.96
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 1K90 · PDBe 1K90 · UniProt P40136 · UniProt P02593
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