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Crystal structure of DNA ligase
Analyse Crystal structure of DNA ligase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EFE
- Type
- protein
- Length
- 313 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase
- EC
- 6.5.1.2
- UniProt
- Q837V6
- Ligands
- NMN, 0OV, SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase (EC 6.5.1.2) | protein | 313 | 41% helix, 23% strand | Q837V6 |
Ligands and binding sites
- NMN · Beta-nicotinamide ribose monophosphate · ligand · chains A
- 0OV · [4-amino-2-{[(1S,2R)-2-methylcyclohexyl]oxy}-5-oxopyrido[2,3-d]pyrimidin-8(5H)-yl]acetonitrile · ligand · chains A
- SO4 · Sulfate ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.73 | 0.83 | 55 | SO4, 0OV |
| 2 | 174 | 0.56 | 0.80 | 27 | empty |
| 3 | 53 | 0.29 | 0.75 | 16 | empty |
Compared structures
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 Q837V6
- Elsewhere: RCSB PDB 4EFE · PDBe 4EFE · UniProt Q837V6
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