Research workbench
Crystal structure of vibrio cholerae dncv cyclic AMP-gmp synthase in complex with nonhydrolyzable GTP
Analyse Crystal structure of vibrio cholerae dncv cyclic AMP-gmp synthase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TXZ
- Type
- protein
- Length
- 736 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic AMP-gmp synthase
- EC
- 2.7.7.86
- UniProt
- Q9KVG7
- Ligands
- G2P, MG
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclic AMP-gmp synthase (EC 2.7.7.86) | protein | 370 | 55% helix, 14% strand | Q9KVG7 |
| B | Cyclic AMP-gmp synthase (EC 2.7.7.86) | protein | 366 | 55% helix, 14% strand | Q9KVG7 |
Ligands and binding sites
- G2P · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.68 | 0.76 | 51 | MG, G2P |
| 2 | 632 | 0.67 | 0.77 | 50 | MG, G2P |
| 3 | 203 | 0.47 | 0.75 | 29 | empty |
| 4 | 55 | 0.47 | 0.85 | 15 | empty |
| 5 | 125 | 0.46 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 269 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4TXZ · Crystal structure of Vibrio cholerae DncV cyclic AMP-GMP synthase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KVG7 · AlphaFold monomer V2.0 prediction for cyclic gmp-AMP synthase (Q9KVG7) · a predicted model of the same protein · 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 Q9KVG7
- Elsewhere: RCSB PDB 4TXZ · PDBe 4TXZ · UniProt Q9KVG7
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