MolNFT v1 · #138565 · protein + DNA
APE1 exonuclease substrate complex with a C/T mismatch and MN2+
5WN5 · DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'): “APE1 exonuclease substrate complex with a C/T mismatch and MN2+”. X-ray diffraction, 2 ligands (MN, NA), 9 pockets (best druggability 0.48). MolNFT v1 #138565 on GenesisL1: 3D…
- PDB
- 5WN5
- Type
- protein + DNA
- Length
- 591 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
- MN, NA
- Pockets
- 9 · best druggability 0.48
Structure
x-ray diffraction · 5 distinct chains · 29% 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 | 273 | 30% helix, 25% strand | P27695 |
| B | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 276 | 28% helix, 25% strand | P27695 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains E, A, D, B
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.48 | 0.81 | 20 | empty |
| 2 | 224 | 0.48 | 0.74 | 25 | empty |
| 3 | 182 | 0.48 | 0.76 | 24 | empty |
| 4 | 193 | 0.47 | 0.75 | 34 | MN |
| 5 | 124 | 0.44 | 0.77 | 24 | empty |
Interfaces
7 interfaces between chains.
- D–B · 554 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–B · 548 Ų buried · 1 hydrogen bond · protein-protein
- E–B · 532 Ų buried · 5 hydrogen bonds · protein-nucleic
- C–E · 485 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- D–E · 417 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5WN5 · APE1 exonuclease substrate complex with a C/T mismatch and Mn2+ · 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 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 5WN5 · PDBe 5WN5 · UniProt P27695
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.