MolNFT v1 · #5167 · protein
A second divalent metal ion in the active site of a new crystal form of human APURINIC/APYRIMIDINIC endonuclease, APE1, and its implications for the catalytic mechanism
1E9N · DNA-(apurinic or apyrimidinic site) lyase: “A second divalent metal ion in the active site of a new crystal form of human APURINIC/APYRIMIDINIC…”. X-ray diffraction, 1 ligand (PB), 5 pockets (best druggability 0.64). MolNFT v1 #5167…
- PDB
- 1E9N
- Type
- protein
- Length
- 548 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-(apurinic or apyrimidinic site) lyase
- EC
- 4.2.99.18
- UniProt
- P27695
- Ligands
- PB
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA-(apurinic or apyrimidinic site) lyase (EC 4.2.99.18) | protein | 274 | 30% helix, 25% strand | P27695 |
Ligands and binding sites
- PB · Lead (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.64 | 0.77 | 37 | empty |
| 2 | 121 | 0.40 | 0.75 | 20 | PB |
| 3 | 128 | 0.40 | 0.75 | 24 | PB |
| 4 | 61 | 0.34 | 0.77 | 14 | empty |
| 5 | 54 | 0.31 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 254 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1E9N · A second divalent metal ion in the active site of a new crystal form of human… · 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 1E9N · PDBe 1E9N · UniProt P27695
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.