Research workbench
APE1 exonuclease product complex
Analyse APE1 exonuclease product complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WN1
- Type
- protein + DNA
- Length
- 591 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-(apurinic or apyrimidinic site) lyase; DNA…
- EC
- 3.1.-.-, 4.2.99.18
- UniProt
- P27695
- Ligands
- NA, CA, CL
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 31% 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 | 276 | 32% helix, 24% strand | P27695 |
| B | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 274 | 30% helix, 25% strand | P27695 |
| C | DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') | dna | 11 | — | — |
| D | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*G)-3') | dna | 9 | — | — |
| E | DNA (5'- D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3') | dna | 21 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains B, D, E
- CA · Calcium ion · metal · chains E
- CL · Chloride ion · ion · chains B
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 | 527 | 0.71 | 0.80 | 45 | empty |
| 2 | 397 | 0.59 | 0.76 | 45 | empty |
| 3 | 315 | 0.55 | 0.75 | 34 | empty |
| 4 | 195 | 0.47 | 0.75 | 36 | empty |
| 5 | 85 | 0.41 | 0.78 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 525 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 513 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–E · 488 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- D–E · 414 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- A–C · 268 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
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 5WN1 · PDBe 5WN1 · UniProt P27695
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.