Research workbench
Crystal structure of an adenylyl cyclase MA1120 from mycobacterium avium in complex with ATP and calcium ion
Analyse Crystal structure of an adenylyl cyclase MA1120 from mycobacterium avium in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D15
- Type
- protein
- Length
- 326 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclase
- UniProt
- V7LAR8
- Ligands
- ATP, CA
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclase | protein | 162 | 40% helix, 33% strand | V7LAR8 |
| B | Cyclase | protein | 164 | 40% helix, 32% strand | V7LAR8 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 816 | 0.76 | 0.80 | 65 | ATP, CA |
| 2 | 89 | 0.32 | 0.73 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1016 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5D15 · Crystal structure of an adenylyl cyclase Ma1120 from Mycobacterium avium in complex with… · the same entry in another collection · chain A against A, 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 V7LAR8
- Elsewhere: RCSB PDB 5D15 · PDBe 5D15 · UniProt V7LAR8
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