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Structure of the vibrio cholerae di-nucleotide cyclase (dncv) in complex with GTP and 5MTHFGLU2
Analyse Structure of the vibrio cholerae di-nucleotide cyclase (dncv) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U03
- Type
- protein
- Length
- 774 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
- GTP, TLL, MG
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclic AMP-gmp synthase (EC 2.7.7.86) | protein | 389 | 56% helix, 13% strand | Q9KVG7 |
| B | Cyclic AMP-gmp synthase (EC 2.7.7.86) | protein | 385 | 55% helix, 13% strand | Q9KVG7 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, B
- TLL · N-[4-({[(6S)-2-amino-5-methyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-gamma-glutamyl-L-glutamic acid · 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
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.69 | 0.77 | 56 | GTP, MG |
| 2 | 562 | 0.69 | 0.78 | 44 | TLL |
| 3 | 666 | 0.69 | 0.77 | 54 | GTP, MG |
| 4 | 145 | 0.68 | 0.88 | 22 | TLL |
| 5 | 52 | 0.35 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 584 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4U03 · Structure of the vibrio cholerae di-nucleotide cyclase (DncV) in complex with GTP and… · 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 B 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 4U03 · PDBe 4U03 · UniProt Q9KVG7
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