Research workbench
Structure of adenylation domain of haemophilus influenzae DNA ligases bound to NAD+ in adenylated state.
Analyse Structure of adenylation domain of haemophilus influenzae DNA ligases bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UQ8
- Type
- protein
- Length
- 322 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase
- EC
- 6.5.1.2
- UniProt
- P43813
- Ligands
- NAD, AMP
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase (EC 6.5.1.2) | protein | 322 | 38% helix, 24% strand | P43813 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- 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 | 404 | 0.71 | 0.82 | 45 | AMP |
| 2 | 88 | 0.50 | 0.83 | 23 | empty |
| 3 | 158 | 0.41 | 0.74 | 27 | empty |
| 4 | 76 | 0.39 | 0.78 | 22 | NAD |
| 5 | 53 | 0.25 | 0.73 | 13 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3UQ8 · Structure of adenylation domain of Haemophilus influenzae DNA ligases bound to NAD+ in… · the same entry in another collection · chain A against A, TM-score 1.00
- P43813 · AlphaFold monomer V2.0 prediction for DNA ligase (P43813) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P43813
- Elsewhere: RCSB PDB 3UQ8 · PDBe 3UQ8 · UniProt P43813
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