MolNFT v1 · #98899 · protein
Crystal structure of human APURINIC/APYRIMIDINIC endonuclease 1 with essential MG2+ cofactor
4LND · DNA-(apurinic or apyrimidinic site) lyase: “Crystal structure of human APURINIC/APYRIMIDINIC endonuclease 1 with essential MG2+ cofactor”. X-ray diffraction, 1 ligand (MG), 9 pockets (best druggability 0.72). MolNFT v1 #98899 on…
- PDB
- 4LND
- Type
- protein
- Length
- 825 residues
- Chains
- 3
- 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
- MG
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | DNA-(apurinic or apyrimidinic site) lyase (EC 4.2.99.18) | protein | 275 | 29% helix, 24% strand | P27695 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.72 | 0.82 | 55 | empty |
| 2 | 604 | 0.63 | 0.74 | 59 | MG |
| 3 | 223 | 0.49 | 0.75 | 24 | empty |
| 4 | 114 | 0.42 | 0.77 | 26 | MG |
| 5 | 124 | 0.41 | 0.75 | 23 | MG |
Interfaces
2 interfaces between chains.
- A–B · 673 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 414 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4LND · Crystal structure of human apurinic/apyrimidinic endonuclease 1 with essential Mg2+… · 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 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 4LND · PDBe 4LND · UniProt P27695
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