MolNFT v1 · #45904 · protein + DNA
Structure of catalytically inactive human 8-oxoguanine glycosylase distal crosslink to oxog DNA
2NOL · 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3': “Structure of catalytically inactive human 8-oxoguanine glycosylase distal crosslink to oxog DNA”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.58). MolNFT…
- PDB
- 2NOL
- Type
- protein + DNA
- Length
- 344 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'…
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- O15527
- Ligands
- CA
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3' | dna | 15 | — | — |
| C | 5'-D(*GP*CP*GP*TP*CP*CP*AP*(G42)P*GP*TP*CP*TP*AP*CP*C)-3' | dna | 15 | — | — |
| A | N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 314 | 47% helix, 11% strand | O15527 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.58 | 0.76 | 33 | CA |
| 2 | 70 | 0.46 | 0.83 | 18 | empty |
| 3 | 104 | 0.43 | 0.77 | 18 | empty |
| 4 | 57 | 0.24 | 0.72 | 11 | empty |
Interfaces
3 interfaces between chains.
- C–A · 788 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–C · 619 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- B–A · 455 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2NOL · Structure of catalytically inactive human 8-oxoguanine glycosylase distal crosslink to… · 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 2NOL · PDBe 2NOL · UniProt O15527
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