MolNFT v1 · #144278 · protein + DNA
Human APE1 substrate complex with an A/A mismatch adjacent the thf
6BOQ · DNA-(apurinic or apyrimidinic site) lyase: “Human APE1 substrate complex with an A/A mismatch adjacent the thf”. X-ray diffraction, 10 pockets (best druggability 0.62). MolNFT v1 #144278 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6BOQ
- Type
- protein + DNA
- Length
- 579 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-(apurinic or apyrimidinic site) lyase; 21-mer DNA
- EC
- 3.1.-.-, 4.2.99.18
- UniProt
- P27695
- Pockets
- 10 · best druggability 0.62
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 3.1.-.-, 4.2.99.18) | protein | 271 | 28% helix, 25% strand | P27695 |
| B | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 266 | 31% helix, 26% strand | P27695 |
| D | 21-mer DNA | dna | 21 | — | — |
| V | 21-mer DNA | dna | 21 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.62 | 0.77 | 35 | empty |
| 2 | 190 | 0.51 | 0.78 | 27 | empty |
| 3 | 185 | 0.51 | 0.78 | 24 | empty |
| 4 | 181 | 0.48 | 0.76 | 33 | empty |
| 5 | 96 | 0.48 | 0.81 | 30 | empty |
Interfaces
4 interfaces between chains.
- D–V · 919 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- A–D · 784 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–V · 586 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–B · 561 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6BOQ · Human APE1 substrate complex with an A/A mismatch adjacent the THF · 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 6BOQ · PDBe 6BOQ · UniProt P27695
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