Research workbench
Crystal structure of human DNA ligase IV-artemis complex (mercury derivative)
Analyse Crystal structure of human DNA ligase IV-artemis complex (mercury derivative) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W1B
- Type
- protein
- Length
- 599 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase 4; Artemis-derived peptide
- EC
- 6.5.1.1
- UniProt
- P49917, Q96SD1
- Ligands
- AMP, HG, SO4
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase 4 (EC 6.5.1.1) | protein | 589 | 37% helix, 22% strand | P49917 |
| B | Artemis-derived peptide | protein | 10 | 50% helix, 0% strand | Q96SD1 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- HG · Mercury (II) ion · metal · 9 copies · chains A
- SO4 · Sulfate ion · ion · 10 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.68 | 0.81 | 52 | HG |
| 2 | 127 | 0.56 | 0.83 | 21 | SO4 |
| 3 | 111 | 0.54 | 0.83 | 15 | empty |
| 4 | 82 | 0.40 | 0.78 | 16 | empty |
| 5 | 100 | 0.40 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 452 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3W1B · Crystal Structure of Human DNA ligase IV-Artemis Complex (Mercury Derivative) · the same entry in another collection · chain A against A, TM-score 1.00
- P49917 · AlphaFold monomer V2.0 prediction for DNA ligase 4 (P49917) · a predicted model of the same protein · chain A against A, TM-score 0.76
- Q96SD1 · AlphaFold monomer V2.0 prediction for protein artemis (Q96SD1) · a predicted model of the same protein · chain B against A, TM-score 0.53
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
- Every structure of UniProt Q96SD1
- Elsewhere: RCSB PDB 3W1B · PDBe 3W1B · UniProt P49917 · UniProt Q96SD1
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