Research workbench
ATP-dependent DNA ligase from pyrococcus furiosus
Analyse ATP-dependent DNA ligase from pyrococcus furiosus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CFM
- Type
- protein
- Length
- 561 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermostable DNA ligase
- EC
- 6.5.1.1
- UniProt
- P56709
- Ligands
- AMP, MG
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thermostable DNA ligase (EC 6.5.1.1) | protein | 561 | 43% helix, 22% strand | P56709 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.78 | 0.90 | 40 | MG, AMP |
| 2 | 820 | 0.70 | 0.76 | 66 | empty |
| 3 | 260 | 0.65 | 0.82 | 31 | empty |
| 4 | 88 | 0.41 | 0.78 | 15 | empty |
| 5 | 85 | 0.34 | 0.74 | 12 | empty |
Modifications
Observed in the structure: 16 modified (engineered).
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 P56709
- Elsewhere: RCSB PDB 2CFM · PDBe 2CFM · UniProt P56709
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.