Research workbench
APE1 mn-bound product complex with abasic ribonucleotide DNA
Analyse APE1 mn-bound product complex with abasic ribonucleotide DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LPH
- Type
- protein + DNA
- Length
- 586 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-(apurinic or apyrimidinic site) lyase; DNA (5'…
- EC
- 3.1.-.-, 4.2.99.18
- UniProt
- P27695
- Ligands
- MN
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 273 | 30% helix, 25% strand | P27695 |
| C | DNA (5'- D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3') | dna | 21 | — | — |
| D | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 271 | 28% helix, 25% strand | P27695 |
| E | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') | dna | 10 | — | — |
| A | DNA (5'-R(P*N)-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') | dna | 11 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains D, E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.71 | 0.75 | 66 | empty |
| 2 | 242 | 0.55 | 0.77 | 31 | empty |
| 3 | 218 | 0.51 | 0.76 | 33 | empty |
| 4 | 82 | 0.44 | 0.80 | 14 | empty |
| 5 | 67 | 0.37 | 0.78 | 16 | empty |
Interfaces
7 interfaces between chains.
- C–D · 618 Ų buried · 9 hydrogen bonds · protein-nucleic
- D–A · 573 Ų buried · 22 hydrogen bonds · protein-nucleic
- C–A · 466 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- C–E · 457 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- D–E · 248 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 7LPH · APE1 Mn-bound product complex with abasic ribonucleotide DNA · the same entry in another collection · chain C against C, 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 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 7LPH · PDBe 7LPH · UniProt P27695
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