MolNFT v1 · #131328 · protein
Pandda analysis group deposition -- crystal structure of DCLRE1A in complex with FMOPL000166A
5Q1V · DNA cross-link repair 1A protein: “Pandda analysis group deposition -- crystal structure of DCLRE1A in complex with FMOPL000166A”. X-ray diffraction, 2 ligands (AXS, NI), 5 pockets (best druggability 0.59). MolNFT v1 #131328 on…
- PDB
- 5Q1V
- Type
- protein
- Length
- 341 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA cross-link repair 1A protein
- UniProt
- Q6PJP8
- Ligands
- AXS, NI
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA cross-link repair 1A protein | protein | 341 | 34% helix, 22% strand | Q6PJP8 |
Ligands and binding sites
- AXS · 1-(4-fluorophenyl)-~{N}-[[(2~{R})-oxolan-2-yl]methyl]methanamine · ligand · chains A
- NI · Nickel (II) ion · metal · chains A
- MLI · Malonate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.59 | 0.80 | 41 | MLI |
| 2 | 89 | 0.39 | 0.77 | 22 | empty |
| 3 | 102 | 0.34 | 0.73 | 20 | empty |
| 4 | 67 | 0.32 | 0.75 | 17 | empty |
| 5 | 51 | 0.30 | 0.76 | 14 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
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 5Q1V · PDBe 5Q1V · UniProt Q6PJP8
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