Research workbench
APE1 exonuclease substrate complex with phosphoglycolate
Analyse APE1 exonuclease substrate complex with phosphoglycolate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WN2
- Type
- protein + DNA
- Length
- 593 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
- Ligands
- PGA, NA, CA
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 276 | 30% helix, 24% 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*G)-3') | dna | 9 | — | — |
| E | DNA (5'- D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3') | 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.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.73 | 0.82 | 45 | NA, PGA |
| 2 | 299 | 0.59 | 0.77 | 41 | empty |
| 3 | 305 | 0.54 | 0.75 | 29 | empty |
| 4 | 174 | 0.44 | 0.74 | 27 | empty |
| 5 | 88 | 0.42 | 0.79 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 520 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 517 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–E · 481 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- D–E · 415 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- A–D · 335 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.