MolNFT v1 · #138562 · protein + DNA
APE1 exonuclease substrate complex with phosphoglycolate
5WN2: “APE1 exonuclease substrate complex with phosphoglycolate”. X-ray diffraction, 3 ligands (PGA, NA, CA). MolNFT v1 #138562 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WN2
- Type
- protein + DNA
- Length
- 593 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- P27695
- Ligands
- PGA, NA, CA
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | — | protein | 276 | — | P27695 |
| C | — | dna | 11 | — | — |
| D | — | dna | 9 | — | — |
| E | — | dna | 21 | — | — |
Ligands and binding sites
- PGA · 2-phosphoglycolic acid · ligand · chains A, D
- NA · Sodium ion · metal · 2 copies · chains A, D, E
- CA · Calcium ion · metal · 2 copies · chains E
- EDO · 1,2-ethanediol · additive · 4 copies · chains B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5WN2 · APE1 exonuclease substrate complex with phosphoglycolate · 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 B 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 5WN2 · PDBe 5WN2 · UniProt P27695
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