MolNFT v1 · #39049 · protein + DNA
O6-METHYL:C pair in the polymerase-10 basepair position
2HHS · 5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3': “O6-METHYL:C pair in the polymerase-10 basepair position”. X-ray diffraction, 4 ligands (GLC, FRU, MG), 10 pockets (best druggability 0.72). MolNFT v1 #39049 on GenesisL1: 3D…
- PDB
- 2HHS
- Type
- protein + DNA
- Length
- 607 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
- 10 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 56% 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(*CP*CP*TP*GP*AP*CP*TP*CP*GP*CP*AP*TP*GP*A)-3' | dna | 14 | — | — |
| 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 · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.72 | 0.86 | 29 | empty |
| 2 | 351 | 0.69 | 0.82 | 42 | GLC, FRU |
| 3 | 745 | 0.69 | 0.76 | 69 | SO4, MG |
| 4 | 169 | 0.47 | 0.75 | 18 | empty |
| 5 | 107 | 0.44 | 0.78 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–A · 879 Ų buried · 23 hydrogen bonds · protein-nucleic
- C–A · 865 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–C · 616 Ų buried · 53 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2HHS · O6-methyl:C 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 2HHS · PDBe 2HHS · UniProt Q5KWC1
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