MolNFT v1 · #116498 · protein + DNA
Human APE1 E96Q/D210N mismatch substrate complex
5DFJ · DNA-(apurinic or apyrimidinic site) lyase: “Human APE1 E96Q/D210N mismatch substrate complex”. X-ray diffraction, 1 ligand (CL), 6 pockets (best druggability 0.66). MolNFT v1 #116498 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5DFJ
- Type
- protein + DNA
- Length
- 583 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-(apurinic or apyrimidinic site) lyase; DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(3DR)…
- EC
- 4.2.99.18
- UniProt
- P27695
- Ligands
- CL
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-(apurinic or apyrimidinic site) lyase (EC 4.2.99.18) | protein | 276 | 29% helix, 24% strand | P27695 |
| B | DNA-(apurinic or apyrimidinic site) lyase (EC 4.2.99.18) | protein | 265 | 30% helix, 25% strand | P27695 |
| P | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(3DR) P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') | dna | 21 | — | — |
| V | DNA (5'- D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3') | dna | 21 | — | — |
Ligands and binding sites
- CL · Chloride ion · ion · 8 copies · chains A, P, B, V
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.66 | 0.80 | 38 | CL |
| 2 | 312 | 0.58 | 0.77 | 36 | empty |
| 3 | 232 | 0.54 | 0.77 | 30 | empty |
| 4 | 159 | 0.45 | 0.76 | 24 | empty |
| 5 | 93 | 0.38 | 0.76 | 14 | empty |
Interfaces
4 interfaces between chains.
- P–V · 924 Ų buried · 86 hydrogen bonds · nucleic-nucleic
- A–B · 823 Ų buried · 14 hydrogen bonds · protein-protein
- A–P · 795 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–V · 599 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5DFJ · Human APE1 E96Q/D210N mismatch substrate complex · the same entry in another collection · chain A against A, 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 5DFJ · PDBe 5DFJ · UniProt P27695
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