MolNFT v1 · #82351 · protein + DNA
Crystal structure of DNA-glycosylase bound to DNA containing 5- hydroxyuracil
3VK7 · Probable formamidopyrimidine-DNA glycosylase: “Crystal structure of DNA-glycosylase bound to DNA containing 5- hydroxyuracil”. X-ray diffraction, 8 pockets (best druggability 0.71). MolNFT v1 #82351 on GenesisL1: 3D structure…
- PDB
- 3VK7
- Type
- protein + DNA
- Length
- 626 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable formamidopyrimidine-DNA glycosylase; DNA…
- EC
- 3.2.2.23, 4.2.99.18
- UniProt
- Q5UQ00
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable formamidopyrimidine-DNA glycosylase (EC 3.2.2.23, 4.2.99.18) | protein | 288 | 31% helix, 25% strand | Q5UQ00 |
| B | Probable formamidopyrimidine-DNA glycosylase (EC 3.2.2.23, 4.2.99.18) | protein | 286 | 30% helix, 24% strand | Q5UQ00 |
| C, E | DNA (5'-D(*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*G)-3') | dna | 13 | — | — |
| D, F | DNA (5'-D(*CP*GP*TP*CP*CP*AP*(OHU)P*GP*TP*CP*TP*AP*C)-3') | dna | 13 | — | — |
Ligands and binding sites
- FMT · Formic acid · additive · 2 copies · chains B, E, F, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.71 | 0.75 | 79 | empty |
| 2 | 493 | 0.64 | 0.77 | 43 | empty |
| 3 | 346 | 0.58 | 0.76 | 26 | empty |
| 4 | 252 | 0.57 | 0.79 | 19 | FMT |
| 5 | 320 | 0.56 | 0.76 | 28 | empty |
Interfaces
9 interfaces between chains.
- A–D · 773 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–F · 773 Ų buried · 17 hydrogen bonds · protein-nucleic
- E–F · 570 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- A–C · 568 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 560 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3VK7 · Crystal structure of DNA-glycosylase bound to DNA containing 5-Hydroxyuracil · the same entry in another collection · 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 Q5UQ00
- Elsewhere: RCSB PDB 3VK7 · PDBe 3VK7 · UniProt Q5UQ00
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