Research workbench
T:O6-methyl-guanine in the polymerase-2 basepair position
Analyse T:O6-methyl-guanine in the polymerase-2 basepair position in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HHV
- Type
- protein + DNA
- Length
- 607 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*CP*TP*TP*G)-3'; 5'-D(*GP*TP*AP*CP*(6OG)P*AP*GP*CP*TP*GP*AP*T…
- EC
- 2.7.7.7
- UniProt
- Q5KWC1
- Ligands
- GLC, FRU, MG, SO4
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*CP*TP*TP*G)-3' | dna | 12 | — | — |
| C | 5'-D(*GP*TP*AP*CP*(6OG)P*AP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)- 3' | dna | 15 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 580 | 56% helix, 13% strand | Q5KWC1 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 861 | 0.71 | 0.76 | 72 | SO4, MG |
| 2 | 147 | 0.70 | 0.90 | 21 | empty |
| 3 | 386 | 0.69 | 0.82 | 44 | GLC, FRU |
| 4 | 122 | 0.58 | 0.85 | 17 | empty |
| 5 | 124 | 0.48 | 0.79 | 26 | empty |
Interfaces
3 interfaces between chains.
- C–A · 1232 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–A · 887 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–C · 590 Ų buried · 36 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2HHV · T:O6-methyl-guanine in the polymerase-2 basepair position · the same entry in another collection · chain B against B, 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 Q5KWC1
- Elsewhere: RCSB PDB 2HHV · PDBe 2HHV · UniProt Q5KWC1
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