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Human APE1 substrate complex with an C/C mismatch adjacent the thf
Analyse Human APE1 substrate complex with an C/C 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
- 6BOT
- Type
- protein + DNA
- Length
- 578 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
- 7 · best druggability 0.64
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 | 267 | 27% helix, 25% strand | P27695 |
| B | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 269 | 29% helix, 25% strand | P27695 |
| P | 21-mer DNA | dna | 21 | — | — |
| V | 21-mer DNA | dna | 21 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.64 | 0.76 | 65 | empty |
| 2 | 216 | 0.58 | 0.81 | 38 | empty |
| 3 | 220 | 0.51 | 0.76 | 37 | empty |
| 4 | 205 | 0.50 | 0.76 | 24 | empty |
| 5 | 103 | 0.50 | 0.81 | 17 | empty |
Interfaces
4 interfaces between chains.
- P–V · 920 Ų buried · 90 hydrogen bonds · nucleic-nucleic
- A–P · 717 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–B · 526 Ų buried · 6 hydrogen bonds · protein-protein
- A–V · 517 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6BOT · Human APE1 substrate complex with an C/C 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 0.99
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 6BOT · PDBe 6BOT · UniProt P27695
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