Research workbench
DDCTP:O6MEG pair in the polymerase active site (0 position)
Analyse DDCTP:O6MEG pair in the polymerase active site (0 position) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HVH
- Type
- protein + DNA
- Length
- 1,200 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'; 5'-D(*CP*A*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3…
- EC
- 2.7.7.7
- UniProt
- Q5KWC1
- Ligands
- DCT, GLC, FRU, MN, SO4
- Pockets
- 19 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, E | 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3' | dna | 9 | — | — |
| C, F | 5'-D(*CP*A*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3' | dna | 11 | — | — |
| A, D | DNA polymerase I (EC 2.7.7.7) | protein | 580 | 54% helix, 14% strand | Q5KWC1 |
Ligands and binding sites
- DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · 2 copies · chains B, C, A, E, F, D
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A, D
- FRU · beta-D-fructofuranose · sugar · 3 copies · chains A, D
- MN · Manganese (II) ion · metal · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.78 | 0.80 | 71 | MN, DCT |
| 2 | 1095 | 0.75 | 0.78 | 68 | MN, DCT |
| 3 | 669 | 0.72 | 0.79 | 49 | empty |
| 4 | 343 | 0.69 | 0.82 | 43 | GLC, FRU |
| 5 | 237 | 0.68 | 0.85 | 29 | empty |
Interfaces
7 interfaces between chains.
- F–D · 1161 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–A · 1139 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–A · 825 Ų buried · 22 hydrogen bonds · protein-nucleic
- E–D · 818 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–D · 676 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 2HVH · ddCTP:O6MeG pair in the polymerase active site (0 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 2HVH · PDBe 2HVH · UniProt Q5KWC1
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