MolNFT v1 · #181260 · protein + DNA
APE1 product complex with abasic ribonucleotide DNA
7LPG · DNA-(apurinic or apyrimidinic site) lyase: “APE1 product complex with abasic ribonucleotide DNA”. X-ray diffraction, 8 pockets (best druggability 0.71). MolNFT v1 #181260 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7LPG
- Type
- protein + DNA
- Length
- 589 residues
- Chains
- 5
- 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
- 8 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 275 | 27% helix, 24% 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 | 272 | 28% helix, 25% strand | P27695 |
| E | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') | dna | 10 | — | — |
| A | DNA (5'-R(P*N)-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') | dna | 11 | — | — |
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 | 1007 | 0.71 | 0.75 | 63 | empty |
| 2 | 189 | 0.51 | 0.78 | 28 | empty |
| 3 | 173 | 0.49 | 0.78 | 21 | empty |
| 4 | 182 | 0.48 | 0.76 | 30 | empty |
| 5 | 62 | 0.47 | 0.84 | 16 | empty |
Interfaces
7 interfaces between chains.
- C–D · 629 Ų buried · 7 hydrogen bonds · protein-nucleic
- D–A · 584 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–A · 466 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- C–E · 457 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- D–E · 207 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 7LPG · APE1 product complex with abasic ribonucleotide DNA · the same entry in another collection · chain C against C, 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 7LPG · PDBe 7LPG · UniProt P27695
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