Research workbench
Human APURINIC/APYRIMIDINIC endonuclease-1 (APE1) bound to abasic DNA
Analyse Human APURINIC/APYRIMIDINIC endonuclease-1 (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
- 1DE8
- Type
- protein + DNA
- Length
- 596 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*CP*TP*AP*CP*(3DR)P*GP*AP*TP*CP*G)- 3'); DNA…
- EC
- 4.2.99.18
- UniProt
- P27695
- Pockets
- 8 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, U | DNA (5'-D(*GP*CP*TP*AP*CP*(3DR)P*GP*AP*TP*CP*G)- 3') | dna | 11 | — | — |
| Y, V | DNA (5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP*C)-3') | dna | 11 | — | — |
| B, A | Major APURINIC/APYRIMIDINIC endonuclease (EC 4.2.99.18) | protein | 276 | 26% helix, 24% strand | P27695 |
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 | 89 | 0.53 | 0.85 | 17 | empty |
| 2 | 92 | 0.50 | 0.83 | 17 | empty |
| 3 | 189 | 0.50 | 0.76 | 23 | empty |
| 4 | 150 | 0.47 | 0.77 | 28 | empty |
| 5 | 145 | 0.44 | 0.76 | 19 | empty |
Interfaces
7 interfaces between chains.
- U–A · 748 Ų buried · 21 hydrogen bonds · protein-nucleic
- X–B · 725 Ų buried · 19 hydrogen bonds · protein-nucleic
- V–A · 555 Ų buried · 8 hydrogen bonds · protein-nucleic
- Y–B · 509 Ų buried · 7 hydrogen bonds · protein-nucleic
- U–V · 476 Ų buried · 50 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1DE8 · Human APURINIC/APYRIMIDINIC endonuclease-1 (APE1) bound to abasic DNA · the same entry in another collection · chain A against A, 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 1DE8 · PDBe 1DE8 · UniProt P27695
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