Research workbench
Crystal structure of NAD+-dependent DNA ligase from T. filiformis
Analyse Crystal structure of NAD+-dependent DNA ligase from T. filiformis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DGS
- Type
- protein
- Length
- 1,162 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase
- EC
- 6.5.1.2
- UniProt
- Q9ZHI0
- Ligands
- AMP, ZN
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA ligase (EC 6.5.1.2) | protein | 581 | 37% helix, 21% strand | Q9ZHI0 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.73 | 0.81 | 64 | AMP |
| 2 | 354 | 0.72 | 0.84 | 45 | AMP |
| 3 | 304 | 0.65 | 0.81 | 41 | empty |
| 4 | 296 | 0.64 | 0.80 | 42 | empty |
| 5 | 144 | 0.52 | 0.80 | 25 | empty |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
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 Q9ZHI0
- Elsewhere: RCSB PDB 1DGS · PDBe 1DGS · UniProt Q9ZHI0
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