Research workbench
Human APE1 substrate complex with an A/G mismatch adjacent the thf
Analyse Human APE1 substrate complex with an A/G mismatch adjacent the thf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BOV
- Type
- protein + DNA
- Length
- 581 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
- 6 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 28% 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 | 270 | 27% helix, 25% strand | P27695 |
| B | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 269 | 29% helix, 26% strand | P27695 |
| P | 21-mer DNA | dna | 21 | — | — |
| V | 21-mer DNA | dna | 21 | — | — |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.69 | 0.77 | 80 | PEG |
| 2 | 226 | 0.53 | 0.77 | 27 | empty |
| 3 | 172 | 0.49 | 0.77 | 23 | empty |
| 4 | 164 | 0.46 | 0.76 | 29 | empty |
| 5 | 58 | 0.35 | 0.78 | 15 | empty |
Interfaces
4 interfaces between chains.
- P–V · 917 Ų buried · 80 hydrogen bonds · nucleic-nucleic
- A–P · 786 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–V · 579 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–B · 534 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6BOV · Human APE1 substrate complex with an A/G 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 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 6BOV · PDBe 6BOV · UniProt P27695
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