Research workbench
Structure of the enterobacter cloacae CD-ntase cdnd in complex with ATP
Analyse Structure of the enterobacter cloacae CD-ntase cdnd in complex with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LJL
- Type
- protein
- Length
- 695 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, MG
- Pockets
- 5 · best druggability 0.78
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 | 347 | 50% helix, 12% strand | P0DSP4 |
| B | Cyclic AMP-AMP-gmp synthase (EC 2.7.7.-) | protein | 348 | 49% helix, 12% strand | P0DSP4 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B
- MG · Magnesium ion · metal · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.78 | 0.80 | 104 | empty |
| 2 | 806 | 0.72 | 0.77 | 59 | MG, ATP |
| 3 | 786 | 0.71 | 0.77 | 53 | MG, ATP |
| 4 | 62 | 0.35 | 0.78 | 14 | empty |
| 5 | 53 | 0.34 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 487 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7LJL · Structure of the Enterobacter cloacae CD-NTase CdnD in complex with ATP · 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 0.97
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 7LJL · PDBe 7LJL · UniProt P0DSP4
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