MolNFT v1 · #8853 · protein
A second divalent metal ion in the active site of a new crystal form of human APURINIC/APYRIDINIMIC endonuclease, APE1, and its implications for the catalytic mechanism
1HD7 · DNA-(apurinic or apyrimidinic site) lyase: “A second divalent metal ion in the active site of a new crystal form of human APURINIC/APYRIDINIMIC…”. X-ray diffraction, 1 ligand (PB), 3 pockets (best druggability 0.45). MolNFT v1 #8853…
- PDB
- 1HD7
- Type
- protein
- Length
- 259 residues
- Chains
- 1
- 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
- 3 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-(apurinic or apyrimidinic site) lyase (EC 4.2.99.18) | protein | 259 | 31% helix, 26% strand | P27695 |
Ligands and binding sites
- PB · Lead (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.45 | 0.74 | 34 | PB |
| 2 | 62 | 0.34 | 0.77 | 15 | empty |
| 3 | 67 | 0.32 | 0.75 | 19 | empty |
Compared structures
- 1HD7 · 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 1HD7 · PDBe 1HD7 · UniProt P27695
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