MolNFT v1 · #39050 · protein + DNA
C:O6-methyl-guanine pair in the polymerase-2 basepair position
2HHT · 5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*CP*TP*CP*G)-3': “C:O6-methyl-guanine pair in the polymerase-2 basepair position”. X-ray diffraction, 4 ligands (GLC, FRU, MG), 9 pockets (best druggability 0.75). MolNFT v1 #39050 on GenesisL1: 3D…
- PDB
- 2HHT
- Type
- protein + DNA
- Length
- 606 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*CP*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 0.75
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*CP*TP*CP*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 | 14 | — | — |
| 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 · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.75 | 0.89 | 34 | empty |
| 2 | 372 | 0.69 | 0.82 | 42 | GLC, FRU |
| 3 | 628 | 0.65 | 0.75 | 66 | SO4, MG |
| 4 | 131 | 0.48 | 0.79 | 26 | empty |
| 5 | 112 | 0.36 | 0.73 | 15 | SO4 |
Interfaces
3 interfaces between chains.
- C–A · 1087 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–A · 868 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 590 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2HHT · C:O6-methyl-guanine pair in the polymerase-2 basepair position · 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 Q5KWC1
- Elsewhere: RCSB PDB 2HHT · PDBe 2HHT · UniProt Q5KWC1
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