Research workbench
Pamora tandem diguanylate cyclase - phosphodiesterase, C-di-gmp complex
Analyse Pamora tandem diguanylate cyclase - phosphodiesterase, C-di-gmp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RNH
- Type
- protein
- Length
- 423 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Motility regulator
- EC
- 2.7.7.65, 3.1.4.52
- UniProt
- Q9HVI8
- Ligands
- C2E, MG
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Motility regulator (EC 2.7.7.65, 3.1.4.52) | protein | 423 | 50% helix, 22% strand | Q9HVI8 |
Ligands and binding sites
- C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.65 | 0.80 | 48 | MG, C2E |
| 2 | 58 | 0.30 | 0.75 | 13 | empty |
| 3 | 50 | 0.30 | 0.76 | 13 | empty |
Compared structures
- 4RNH · PaMorA tandem diguanylate cyclase - phosphodiesterase, c-di-GMP complex · the same entry in another collection · 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 Q9HVI8
- Elsewhere: RCSB PDB 4RNH · PDBe 4RNH · UniProt Q9HVI8
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