Research workbench
DNA ligase from the archaeon thermococcus sibiricus
Analyse DNA ligase from the archaeon thermococcus sibiricus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EQ5
- Type
- protein
- Length
- 516 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase
- EC
- 6.5.1.1
- UniProt
- C6A2U9
- Ligands
- AMP
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase (EC 6.5.1.1) | protein | 516 | 39% helix, 25% strand | C6A2U9 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.82 | 0.83 | 104 | empty |
| 2 | 305 | 0.78 | 0.90 | 42 | AMP |
| 3 | 96 | 0.36 | 0.74 | 15 | empty |
| 4 | 60 | 0.32 | 0.76 | 16 | empty |
| 5 | 52 | 0.27 | 0.74 | 15 | empty |
Compared structures
- 4EQ5 · DNA ligase from the archaeon Thermococcus sibiricus · 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 C6A2U9
- Elsewhere: RCSB PDB 4EQ5 · PDBe 4EQ5 · UniProt C6A2U9
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