Research workbench
Crystal structure of human DNA cross-link repair 1A in complex with a cyclic N-hydroxyurea inhibitor
Analyse Crystal structure of human DNA cross-link repair 1A in complex with a cyclic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CG9
- Type
- protein
- Length
- 331 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.68
- Source
- Homo sapiens
- Molecule
- DNA cross-link repair 1A protein
- EC
- 3.5.2.6
- UniProt
- Q6PJP8
- Ligands
- XOB, R3Z, NI, ZN, SO4
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · resolution 1.68 · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA cross-link repair 1A protein (EC 3.5.2.6) | protein | 331 | 32% helix, 23% strand | Q6PJP8 |
Ligands and binding sites
- XOB · 1-[[(3~{R})-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]-3-oxidanyl-thieno[3,2-d]pyrimidine-2,4-dione · ligand · chains A
- R3Z · 1-[(2S)-2,3-dihydro-1,4-benzodioxin-2-ylmethyl]-3-hydroxythieno[3,2-d]pyrimidine-2,4(1H,3H)-dione · ligand · chains A
- NI · Nickel (II) ion · metal · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.56 | 0.79 | 43 | R3Z, ZN, SO4 |
| 2 | 116 | 0.37 | 0.74 | 21 | empty |
| 3 | 68 | 0.32 | 0.74 | 16 | empty |
| 4 | 68 | 0.31 | 0.74 | 17 | empty |
Compared structures
- Q6PJP8 · AlphaFold monomer V2.0 prediction for DNA cross-link repair 1A protein (Q6PJP8) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q6PJP8
- Elsewhere: RCSB PDB 8CG9 · PDBe 8CG9 · UniProt Q6PJP8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.