MolNFT v1 · #80832 · protein
Crystal structure of human APURINIC/APYRIDINIMIC endonuclease, APE1 in a new crystal form
3U8U · DNA-(apurinic or apyrimidinic site) lyase: “Crystal structure of human APURINIC/APYRIDINIMIC endonuclease, APE1 in a new crystal form”. X-ray diffraction, 2 ligands (MG, CL), 19 pockets (best druggability 0.73). MolNFT v1 #80832 on…
- PDB
- 3U8U
- Type
- protein
- Length
- 1,640 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-(apurinic or apyrimidinic site) lyase
- EC
- 3.1.-.-, 4.2.99.18
- UniProt
- P27695
- Ligands
- MG, CL
- Pockets
- 19 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 275 | 29% helix, 24% strand | P27695 |
| D | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 269 | 28% helix, 25% strand | P27695 |
| E | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 271 | 31% helix, 25% strand | P27695 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 4 copies · chains A, B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.73 | 0.79 | 67 | empty |
| 2 | 801 | 0.67 | 0.75 | 73 | MG, CL |
| 3 | 431 | 0.65 | 0.78 | 34 | empty |
| 4 | 400 | 0.62 | 0.77 | 37 | empty |
| 5 | 63 | 0.62 | 0.92 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 608 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 598 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 517 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 420 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 338 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3U8U · Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form · the same entry in another collection · chain F against F, 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 D 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 3U8U · PDBe 3U8U · UniProt P27695
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