MolNFT v1 · #138560 · protein + DNA
APE1 exonuclease substrate complex with a C/G match
5WN0 · DNA-(apurinic or apyrimidinic site) lyase: “APE1 exonuclease substrate complex with a C/G match”. X-ray diffraction, 9 pockets (best druggability 0.64). MolNFT v1 #138560 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WN0
- Type
- protein + DNA
- Length
- 591 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-(apurinic or apyrimidinic site) lyase; DNA…
- EC
- 3.1.-.-, 4.2.99.18
- UniProt
- P27695
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 276 | 24% helix, 24% strand | P27695 |
| 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(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') | dna | 11 | — | — |
| D | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') | dna | 10 | — | — |
| E | 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 | — | — |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.64 | 0.78 | 49 | empty |
| 2 | 255 | 0.55 | 0.77 | 37 | empty |
| 3 | 186 | 0.49 | 0.77 | 26 | empty |
| 4 | 170 | 0.46 | 0.75 | 30 | empty |
| 5 | 85 | 0.41 | 0.79 | 17 | empty |
Interfaces
7 interfaces between chains.
- A–E · 556 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–C · 479 Ų buried · 5 hydrogen bonds · protein-nucleic
- C–E · 476 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- A–B · 476 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 449 Ų buried · 51 hydrogen bonds · nucleic-nucleic
Compared structures
- 5WN0 · APE1 exonuclease substrate complex with a C/G match · 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 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 5WN0 · PDBe 5WN0 · UniProt P27695
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