MolNFT v1 · #82352 · protein + DNA
Crystal structure of DNA-glycosylase bound to DNA containing thymine glycol
3VK8 · Probable formamidopyrimidine-DNA glycosylase: “Crystal structure of DNA-glycosylase bound to DNA containing thymine glycol”. X-ray diffraction, 7 pockets (best druggability 0.71). MolNFT v1 #82352 on GenesisL1: 3D structure, binding…
- PDB
- 3VK8
- Type
- protein + DNA
- Length
- 628 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
- 7 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable formamidopyrimidine-DNA glycosylase (EC 3.2.2.23, 4.2.99.18) | protein | 288 | 30% helix, 26% strand | Q5UQ00 |
| C, E | DNA (5'-D(*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3') | dna | 13 | — | — |
| D, F | DNA (5'-D(*CP*GP*TP*CP*CP*AP*(CTG)P*GP*TP*CP*TP*AP*C)-3') | dna | 13 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.71 | 0.75 | 78 | empty |
| 2 | 550 | 0.65 | 0.77 | 53 | empty |
| 3 | 247 | 0.57 | 0.79 | 20 | GOL |
| 4 | 330 | 0.57 | 0.76 | 27 | empty |
| 5 | 320 | 0.57 | 0.76 | 35 | empty |
Interfaces
9 interfaces between chains.
- A–D · 794 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–F · 793 Ų buried · 17 hydrogen bonds · protein-nucleic
- E–F · 574 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- C–D · 572 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- A–C · 566 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3VK8 · Crystal structure of DNA-glycosylase bound to DNA containing Thymine glycol · 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 3VK8 · PDBe 3VK8 · UniProt Q5UQ00
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