MolNFT v1 · #69551 · protein + DNA
Structure of human 8-oxoguanine glycosylase 1 bound to fluorninated oxog-containing DNA
3KTU · N-GLYCOSYLASE/DNA lyase: “Structure of human 8-oxoguanine glycosylase 1 bound to fluorninated oxog-containing DNA”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.59). MolNFT v1 #69551 on GenesisL1: 3D structure…
- PDB
- 3KTU
- Type
- protein + DNA
- Length
- 339 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-GLYCOSYLASE/DNA lyase; DNA (5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*C)-3'); DNA…
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- O15527
- Ligands
- CA
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 314 | 48% helix, 12% strand | O15527 |
| B | DNA (5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*C)-3') | dna | 13 | — | — |
| C | DNA (5'-D(*GP*TP*CP*CP*AP*(FDG)P*GP*TP*CP*TP*AP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, C
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 | 423 | 0.59 | 0.76 | 40 | CA |
| 2 | 167 | 0.48 | 0.76 | 23 | empty |
| 3 | 77 | 0.47 | 0.83 | 15 | empty |
| 4 | 72 | 0.29 | 0.74 | 17 | empty |
| 5 | 63 | 0.26 | 0.73 | 9 | empty |
Interfaces
3 interfaces between chains.
- A–C · 791 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 486 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- A–B · 427 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3KTU · Structure of human 8-oxoGuanine Glycosylase 1 bound to fluorninated oxoG-containing DNA · the same entry in another collection · chain A against A, 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 3KTU · PDBe 3KTU · UniProt O15527
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