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crystal structure of cyclic GMP-AMP specifc phosphodiesterases in V.cholerae (V-cGAP3)
Analyse crystal structure of cyclic GMP-AMP specifc phosphodiesterases in V.cholerae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z7C
- Type
- protein
- Length
- 414 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.76
- Source
- Vibrio cholerae O1 biovar El Tor str. N16961
- Molecule
- 3'3'-cGAMP-specific phosphodiesterase 3
- EC
- 3.1.4.-
- UniProt
- Q9KL18
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.76 · 1 distinct chain · 61% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3'3'-cGAMP-specific phosphodiesterase 3 (EC 3.1.4.-) | protein | 414 | 61% helix, 2% strand | Q9KL18 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.77 | 0.83 | 85 | empty |
| 2 | 136 | 0.46 | 0.77 | 24 | empty |
| 3 | 147 | 0.42 | 0.75 | 21 | empty |
| 4 | 131 | 0.41 | 0.75 | 19 | empty |
| 5 | 133 | 0.40 | 0.74 | 22 | empty |
Compared structures
- 5Z7C · Crystal structure of cyclic gmp-AMP specifc phosphodiesterases in V.CHOLERAE (V-CGAP3) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KL18 · AlphaFold monomer V2.0 prediction for 3'3'-cgamp-specific phosphodiesterase 3 (Q9KL18) · a predicted model of the same protein · chain A against A, TM-score 0.74
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 Q9KL18
- Elsewhere: RCSB PDB 5Z7C · PDBe 5Z7C · UniProt Q9KL18
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