MolNFT v1 · #24900 · protein
Crystal structure of NAD+-dependent DNA ligase
1V9P: “Crystal structure of NAD+-dependent DNA ligase”. X-ray diffraction, 2 ligands (AMP, ZN), 7 pockets (best druggability 0.75). MolNFT v1 #24900 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1V9P
- Type
- protein
- Length
- 1,168 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
- 7 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA ligase (EC 6.5.1.2) | protein | 584 | 35% 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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.75 | 0.82 | 66 | AMP |
| 2 | 588 | 0.74 | 0.81 | 68 | AMP |
| 3 | 344 | 0.66 | 0.81 | 48 | empty |
| 4 | 252 | 0.62 | 0.81 | 39 | empty |
| 5 | 107 | 0.44 | 0.78 | 19 | 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 Q9ZHI0
- Elsewhere: RCSB PDB 1V9P · PDBe 1V9P · UniProt Q9ZHI0
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