Research workbench
Cyclic trinucleotide synthase cdnd in complex with ATP and ADP
Analyse Cyclic trinucleotide synthase cdnd in complex with ATP and ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D4O
- Type
- protein
- Length
- 693 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic AMP-AMP-gmp synthase
- EC
- 2.7.7.-
- UniProt
- P0DSP4
- Ligands
- ATP, ADP, MG
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclic AMP-AMP-gmp synthase (EC 2.7.7.-) | protein | 346 | 49% helix, 12% strand | P0DSP4 |
| B | Cyclic AMP-AMP-gmp synthase (EC 2.7.7.-) | protein | 347 | 49% helix, 12% strand | P0DSP4 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.73 | 0.83 | 53 | ATP, ADP, MG |
| 2 | 227 | 0.65 | 0.83 | 28 | ATP, ADP |
| 3 | 185 | 0.61 | 0.83 | 35 | GOL |
| 4 | 51 | 0.51 | 0.88 | 19 | empty |
| 5 | 57 | 0.43 | 0.82 | 14 | GOL |
Interfaces
1 interface between chains.
- A–B · 492 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7D4O · cyclic trinucleotide synthase CdnD in complex with ATP and ADP · the same entry in another collection · chain A against A, TM-score 1.00
- P0DSP4 · AlphaFold monomer V2.0 prediction for cyclic AMP-AMP-gmp synthase (P0DSP4) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P0DSP4
- Elsewhere: RCSB PDB 7D4O · PDBe 7D4O · UniProt P0DSP4
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