Research workbench
Crystal structure of the dbd domain of human DNA ligase IV bound to artemis peptide
Analyse Crystal structure of the dbd domain of human DNA ligase IV bound to artemis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HTP
- Type
- protein
- Length
- 457 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase 4; Protein artemis
- EC
- 6.5.1.1, 3.1.-.-
- UniProt
- P49917, Q96SD1
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 62% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase 4 (EC 6.5.1.1) | protein | 221 | 63% helix, 1% strand | P49917 |
| B | DNA ligase 4 (EC 6.5.1.1) | protein | 222 | 64% helix, 1% strand | P49917 |
| C | Protein artemis (EC 3.1.-.-) | protein | 10 | 30% helix, 0% strand | Q96SD1 |
| E | Protein artemis (EC 3.1.-.-) | protein | 4 | 0% helix, 0% strand | Q96SD1 |
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 | 76 | 0.73 | 0.97 | 18 | empty |
| 2 | 265 | 0.53 | 0.76 | 40 | empty |
| 3 | 102 | 0.39 | 0.76 | 21 | empty |
| 4 | 63 | 0.30 | 0.75 | 15 | empty |
| 5 | 51 | 0.25 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 688 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 453 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 258 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4HTP · Crystal structure of the DBD domain of human DNA ligase IV bound to Artemis peptide · the same entry in another collection · chain E against E, 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 0.98
- Q96SD1 · AlphaFold monomer V2.0 prediction for protein artemis (Q96SD1) · a predicted model of the same protein · chain E against A, TM-score 0.86
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 4HTP · PDBe 4HTP · UniProt P49917 · UniProt Q96SD1
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