Research workbench
Crystal structure of human APE1 bound to abasic DNA
Analyse Crystal structure of human APE1 bound to abasic DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DEW
- Type
- protein + DNA
- Length
- 615 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*CP*GP*TP*CP*CP*(3DR) P*CP*GP*AP*CP*GP*AP*CP*G)-3'…
- EC
- 4.2.99.18
- UniProt
- P27695
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, U | 5'-D(*GP*CP*GP*TP*CP*CP*(3DR) P*CP*GP*AP*CP*GP*AP*CP*G)-3' | dna | 15 | — | — |
| Y, V | 5'-D(*GP*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*GP*C)- 3' | dna | 14 | — | — |
| A | Major APURINIC/APYRIMIDINIC endonuclease (EC 4.2.99.18) | protein | 278 | 29% helix, 24% strand | P27695 |
| B | Major APURINIC/APYRIMIDINIC endonuclease (EC 4.2.99.18) | protein | 279 | 26% helix, 25% strand | P27695 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.66 | 0.76 | 65 | empty |
| 2 | 292 | 0.55 | 0.76 | 35 | empty |
| 3 | 200 | 0.48 | 0.75 | 21 | empty |
| 4 | 113 | 0.47 | 0.80 | 18 | empty |
| 5 | 98 | 0.40 | 0.77 | 20 | empty |
Interfaces
7 interfaces between chains.
- X–B · 769 Ų buried · 15 hydrogen bonds · protein-nucleic
- U–A · 759 Ų buried · 17 hydrogen bonds · protein-nucleic
- V–A · 636 Ų buried · 9 hydrogen bonds · protein-nucleic
- Y–B · 631 Ų buried · 7 hydrogen bonds · protein-nucleic
- X–Y · 606 Ų buried · 69 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1DEW · Crystal structure of human APE1 bound to abasic DNA · the same entry in another collection · chain B against B, TM-score 1.00
- P27695 · AlphaFold monomer V2.0 prediction for DNA-(apurinic or apyrimidinic site) endonuclease… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P27695
- Elsewhere: RCSB PDB 1DEW · PDBe 1DEW · UniProt P27695
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