MolNFT v1 · #15388 · protein + DNA
Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase
1N39 · DNA complement strand: “Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.71). MolNFT v1 #15388 on GenesisL1: 3D…
- PDB
- 1N39
- Type
- protein + DNA
- Length
- 344 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA complement strand; DNA inhibitor strand; N-GLYCOSYLASE/DNA lyase
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- O15527
- Ligands
- CA
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA complement strand | dna | 15 | — | — |
| C | DNA inhibitor strand | dna | 15 | — | — |
| A | N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 314 | 49% helix, 12% strand | O15527 |
Ligands and binding sites
- CA · Calcium ion · metal · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.71 | 0.98 | 20 | empty |
| 2 | 429 | 0.60 | 0.76 | 37 | CA |
| 3 | 203 | 0.51 | 0.76 | 31 | empty |
| 4 | 84 | 0.50 | 0.83 | 18 | empty |
| 5 | 176 | 0.42 | 0.73 | 37 | empty |
Interfaces
3 interfaces between chains.
- C–A · 640 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–C · 608 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- B–A · 451 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1N39 · Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine… · the same entry in another collection · chain B against B, TM-score 1.00
- O15527 · AlphaFold monomer V2.0 prediction for N-GLYCOSYLASE/DNA lyase (O15527) · 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 O15527
- Elsewhere: RCSB PDB 1N39 · PDBe 1N39 · UniProt O15527
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