Research workbench
Human APE1 endonuclease with bound abasic DNA and MN2+ ion
Analyse Human APE1 endonuclease with bound abasic DNA and MN2+ ion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DE9
- Type
- protein + DNA
- Length
- 588 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*TP*AP*C)-3'; 5'-D(P*(3DR)P*GP*AP*TP*C)-3'; 5'-D(*GP*AP*TP*CP*GP*GP*TP*AP*G)-3'…
- EC
- 4.2.99.18
- UniProt
- P27695
- Ligands
- MN
- Pockets
- 2 · best druggability 0.28
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, U | 5'-D(*CP*TP*AP*C)-3' | dna | 4 | — | — |
| Y, V | 5'-D(P*(3DR)P*GP*AP*TP*C)-3' | dna | 5 | — | — |
| Z, W | 5'-D(*GP*AP*TP*CP*GP*GP*TP*AP*G)-3' | dna | 9 | — | — |
| A, B | Major APURINIC/APYRIMIDINIC endonuclease (EC 4.2.99.18) | protein | 276 | 27% helix, 26% strand | P27695 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains X, Y, A, U, V, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.28 | 0.73 | 14 | empty |
| 2 | 63 | 0.28 | 0.73 | 15 | empty |
Interfaces
12 interfaces between chains.
- V–B · 610 Ų buried · 17 hydrogen bonds · protein-nucleic
- Y–A · 591 Ų buried · 14 hydrogen bonds · protein-nucleic
- Z–A · 501 Ų buried · 6 hydrogen bonds · protein-nucleic
- W–B · 475 Ų buried · 7 hydrogen bonds · protein-nucleic
- U–B · 223 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1DE9 · Human APE1 endonuclease with bound abasic DNA and MN2+ ion · 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 1DE9 · PDBe 1DE9 · UniProt P27695
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