Research workbench
Structure of rhodothermus marinus cdne C-ump-AMP synthase with apcpp and upnpp
Analyse Structure of rhodothermus marinus cdne C-ump-AMP synthase with apcpp and upnpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E0L
- Type
- protein
- Length
- 292 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CGAS/DNCV-like nucleotidyltransferase in E. COLI homolog
- UniProt
- G2SLH8
- Ligands
- APC, 2KH, MG
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CGAS/DNCV-like nucleotidyltransferase in E. COLI homolog | protein | 292 | 44% helix, 18% strand | G2SLH8 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A
- 2KH · 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine · ligand · chains A
- MG · Magnesium ion · metal · 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 | 518 | 0.65 | 0.77 | 43 | MG, APC, 2KH |
| 2 | 87 | 0.36 | 0.75 | 15 | empty |
Compared structures
- 6E0L · Structure of Rhodothermus marinus CdnE c-UMP-AMP synthase with Apcpp and Upnpp · the same entry in another collection · chain A against A, TM-score 1.00
- G2SLH8 · AlphaFold monomer V2.0 prediction for cyclic ump-AMP synthase (G2SLH8) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 G2SLH8
- Elsewhere: RCSB PDB 6E0L · PDBe 6E0L · UniProt G2SLH8
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