MolNFT v1 · #131316 · protein
Pandda analysis group deposition -- crystal structure of DCLRE1A in complex with FMSOA000341B
5Q1J · DNA cross-link repair 1A protein: “Pandda analysis group deposition -- crystal structure of DCLRE1A in complex with FMSOA000341B”. X-ray diffraction, 2 ligands (9KS, NI), 5 pockets (best druggability 0.59). MolNFT v1 #131316 on…
- PDB
- 5Q1J
- 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
- 9KS, NI
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA cross-link repair 1A protein | protein | 341 | 35% helix, 22% strand | Q6PJP8 |
Ligands and binding sites
- 9KS · N-(2-hydroxyphenyl)acetamide · 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 | 231 | 0.59 | 0.80 | 41 | MLI |
| 2 | 91 | 0.38 | 0.76 | 21 | empty |
| 3 | 77 | 0.34 | 0.75 | 18 | empty |
| 4 | 97 | 0.34 | 0.73 | 19 | empty |
| 5 | 53 | 0.30 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5Q1J · PanDDA analysis group deposition -- Crystal Structure of DCLRE1A in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 5Q1J · PDBe 5Q1J · UniProt Q6PJP8
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