MolNFT v1 · #109994 · protein
Crystal structure of vibrio cholerae dncv 3'-deoxy GTP bound form
4XJ5 · Cyclic AMP-gmp synthase: “Crystal structure of vibrio cholerae dncv 3'-deoxy GTP bound form”. X-ray diffraction, 3 ligands (GH3, MG, NA), 2 pockets (best druggability 0.70). MolNFT v1 #109994 on GenesisL1: 3D structure, binding…
- PDB
- 4XJ5
- Type
- protein
- Length
- 367 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic AMP-gmp synthase
- EC
- 2.7.7.-
- UniProt
- Q9KVG7
- Ligands
- GH3, MG, NA
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclic AMP-gmp synthase (EC 2.7.7.-) | protein | 367 | 56% helix, 15% strand | Q9KVG7 |
Ligands and binding sites
- GH3 · 3'-deoxy-guanosine-5'-triphosphate · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 10 copies · chains A
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 | 731 | 0.70 | 0.77 | 55 | MG, EDO, GH3 |
| 2 | 55 | 0.47 | 0.85 | 15 | EDO |
Compared structures
- 4XJ5 · Crystal structure of Vibrio cholerae DncV 3'-deoxy GTP bound form · 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 0.99
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 4XJ5 · PDBe 4XJ5 · UniProt Q9KVG7
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