Research workbench
APE1 F266A exonuclease substrate complex with a C/T mismatch
Analyse APE1 F266A exonuclease substrate complex with a C/T mismatch in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WN3
- Type
- protein + DNA
- Length
- 593 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'); DNA…
- EC
- 3.1.-.-, 4.2.99.18
- UniProt
- P27695
- Ligands
- NA, CA, CL
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 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*(DV3))-3') | dna | 10 | — | — |
| E | DNA (5'- D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3') | dna | 21 | — | — |
| A | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 276 | 30% helix, 24% strand | P27695 |
| B | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 275 | 30% helix, 25% strand | P27695 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B
- CA · Calcium ion · metal · chains D
- CL · Chloride ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.65 | 0.80 | 32 | CA |
| 2 | 236 | 0.59 | 0.79 | 32 | empty |
| 3 | 280 | 0.53 | 0.75 | 28 | empty |
| 4 | 226 | 0.50 | 0.76 | 33 | empty |
| 5 | 91 | 0.40 | 0.77 | 19 | empty |
Interfaces
7 interfaces between chains.
- E–B · 547 Ų buried · 6 hydrogen bonds · protein-nucleic
- D–B · 540 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–B · 524 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 473 Ų buried · 32 hydrogen bonds · nucleic-nucleic
- D–E · 422 Ų buried · 44 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5WN3 · APE1 F266A exonuclease substrate complex with a C/T mismatch · the same entry in another collection · chain D against D, 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 5WN3 · PDBe 5WN3 · UniProt P27695
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