Research workbench
O6-methyl-GUANINE:T pair in the polymerase-10 basepair position
Analyse O6-methyl-GUANINE:T pair in the polymerase-10 basepair position in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HHQ
- Type
- protein + DNA
- Length
- 608 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'…
- EC
- 2.7.7.7
- UniProt
- Q5KWC1
- Ligands
- GLC, FRU, MG, SO4
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3' | dna | 13 | — | — |
| C | 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP*TP*AP*TP*GP*A)-3' | dna | 15 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 580 | 55% helix, 13% strand | Q5KWC1 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A, C
- FRU · beta-D-fructofuranose · sugar · 3 copies · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.70 | 0.82 | 42 | GLC, FRU |
| 2 | 114 | 0.69 | 0.92 | 20 | empty |
| 3 | 351 | 0.65 | 0.80 | 40 | SO4, MG |
| 4 | 333 | 0.50 | 0.72 | 33 | empty |
| 5 | 116 | 0.47 | 0.80 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–A · 1065 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–A · 919 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–C · 622 Ų buried · 48 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2HHQ · O6-methyl-guanine:T pair in the polymerase-10 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 2HHQ · PDBe 2HHQ · UniProt Q5KWC1
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