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Crystal structure of human DNA ligase IV
Analyse Crystal structure of human DNA ligase IV in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W5O
- Type
- protein
- Length
- 1,156 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase 4
- EC
- 6.5.1.1
- UniProt
- P49917
- Ligands
- ATP, SO4
- Pockets
- 16 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase 4 (EC 6.5.1.1) | protein | 577 | 35% helix, 22% strand | P49917 |
| B | DNA ligase 4 (EC 6.5.1.1) | protein | 579 | 36% helix, 22% strand | P49917 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 24 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.62 | 0.78 | 46 | empty |
| 2 | 259 | 0.56 | 0.77 | 36 | SO4 |
| 3 | 128 | 0.55 | 0.82 | 19 | ATP |
| 4 | 142 | 0.52 | 0.80 | 24 | ATP |
| 5 | 169 | 0.47 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 133 Ų buried · 1 hydrogen bond · protein-protein
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 P49917
- Elsewhere: RCSB PDB 3W5O · PDBe 3W5O · UniProt P49917
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