MolNFT v1 · #107896 · protein + DNA
A new bio-isosteric base pair based on reversible bonding
4UQG · DNA polymerase: “A new bio-isosteric base pair based on reversible bonding”. X-ray diffraction, 3 ligands (GLC, FRU, SO4), 11 pockets (best druggability 0.74). MolNFT v1 #107896 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4UQG
- Type
- protein + DNA
- Length
- 599 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; 5'-D(*GP*AP*CP*C T0TP*TP*CP*CP*CP*TP)-3'; 5'-D(*AP*GP*GP*GP*A…
- EC
- 2.7.7.7
- UniProt
- E1C9K5
- Ligands
- GLC, FRU, SO4
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 579 | 56% helix, 13% strand | E1C9K5 |
| B | 5'-D(*GP*AP*CP*C T0TP*TP*CP*CP*CP*TP)-3' | dna | 10 | — | — |
| C | 5'-D(*AP*GP*GP*GP*A SAYP*GP*GP*TP*CP)-3' | dna | 10 | — | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains A
- FRU · beta-D-fructofuranose · sugar · chains A
- SO4 · Sulfate ion · ion · 4 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.74 | 0.85 | 32 | empty |
| 2 | 368 | 0.70 | 0.82 | 48 | GLC, FRU, SO4 |
| 3 | 411 | 0.65 | 0.79 | 44 | empty |
| 4 | 57 | 0.54 | 0.88 | 15 | empty |
| 5 | 119 | 0.47 | 0.79 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 833 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 703 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–C · 473 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4UQG · A new bio-isosteric base pair based on reversible bonding · 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 E1C9K5
- Elsewhere: RCSB PDB 4UQG · PDBe 4UQG · UniProt E1C9K5
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