MolNFT v1 · #181262 · protein + DNA
APE1 phosphorothioate substrate complex with abasic ribonucleotide DNA
7LPI · DNA-(apurinic or apyrimidinic site) lyase: “APE1 phosphorothioate substrate complex with abasic ribonucleotide DNA”. X-ray diffraction, 7 pockets (best druggability 0.72). MolNFT v1 #181262 on GenesisL1: 3D structure, binding sites…
- PDB
- 7LPI
- Type
- protein + DNA
- Length
- 586 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-(apurinic or apyrimidinic site) lyase; DNA (5'…
- EC
- 3.1.-.-, 4.2.99.18
- UniProt
- P27695
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 273 | 27% helix, 25% strand | P27695 |
| C | DNA (5'- D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3') | dna | 21 | — | — |
| D | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 271 | 30% helix, 25% strand | P27695 |
| E | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-R(P*(YA4))- D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') | dna | 21 | — | — |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.72 | 0.75 | 59 | empty |
| 2 | 223 | 0.55 | 0.78 | 30 | empty |
| 3 | 181 | 0.47 | 0.76 | 30 | empty |
| 4 | 86 | 0.39 | 0.77 | 14 | empty |
| 5 | 57 | 0.37 | 0.79 | 14 | empty |
Interfaces
4 interfaces between chains.
- C–E · 911 Ų buried · 87 hydrogen bonds · nucleic-nucleic
- D–E · 814 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–D · 599 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–D · 164 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7LPI · APE1 phosphorothioate substrate complex with abasic ribonucleotide 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 D 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 P27695
- Elsewhere: RCSB PDB 7LPI · PDBe 7LPI · UniProt P27695
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