MolNFT v1 · #116026 · protein
Crystal structure of an adenylyl cyclase MA1120 from mycobacterium avium in complex with ATP and calcium ion
5D15: “Crystal structure of an adenylyl cyclase MA1120 from mycobacterium avium in complex with ATP and calcium ion”. X-ray diffraction, 2 ligands (ATP, CA), 2 pockets (best druggability 0.76). MolNFT v1 #116026 on GenesisL1: 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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