MolNFT v1 · #94333 · protein
Crystal structure of the dbd domain of human DNA ligase IV bound to artemis peptide
4HTP · DNA ligase 4: “Crystal structure of the dbd domain of human DNA ligase IV bound to artemis peptide”. X-ray diffraction, 5 pockets (best druggability 0.73). MolNFT v1 #94333 on GenesisL1: 3D structure, binding sites and pockets in…
- 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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