Research workbench
Structure of elizabethkingia meningoseptica cdne cyclic dinucleotide synthase with PPPA[3'-5']PA
Analyse Structure of elizabethkingia meningoseptica cdne cyclic dinucleotide synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E0O
- Type
- protein + RNA
- Length
- 277 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CGAS/DNCV-like nucleotidyltransferase in E. COLI homolog; RNA (5'-D(*(ATP))-R(P*A)-3')
- Ligands
- MG
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CGAS/DNCV-like nucleotidyltransferase in E. COLI homolog | protein | 273 | 47% helix, 18% strand | — |
| C, B | RNA (5'-D(*(ATP))-R(P*A)-3') | rna | 2 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, C
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 | 288 | 0.67 | 0.82 | 35 | empty |
| 2 | 187 | 0.46 | 0.75 | 28 | empty |
Interfaces
2 interfaces between chains.
- A–C · 503 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–B · 194 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6E0O · Structure of Elizabethkingia meningoseptica CdnE cyclic dinucleotide synthase with… · 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
- Elsewhere: RCSB PDB 6E0O · PDBe 6E0O
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