MolNFT v1 · #89546 · protein + DNA
Ternary complex of bacillus DNA polymerase I large fragment F710Y, DNA duplex, and rctp (paired with dg of template) in presence of MN2+
4DSF: “Ternary complex of bacillus DNA polymerase I large fragment F710Y, DNA duplex, and rctp (paired with dg of…”. X-ray diffraction, 2 ligands (CTP, SO4), 19 pockets (best druggability 0.75). MolNFT v1 #89546 on GenesisL1: 3D structure…
- PDB
- 4DSF
- Type
- protein + DNA
- Length
- 1,164 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q5KWC1
- Ligands
- CTP, SO4
- Pockets
- 19 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 546 | 53% helix, 14% strand | Q5KWC1 |
| D | DNA polymerase (EC 2.7.7.7) | protein | 579 | 54% helix, 14% strand | Q5KWC1 |
| B, E | DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3') | dna | 9 | — | — |
| C | DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3') | dna | 9 | — | — |
| F | DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · chains D, E, F
- SO4 · Sulfate ion · ion · 4 copies · chains 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.75 | 0.79 | 71 | CTP |
| 2 | 862 | 0.73 | 0.78 | 58 | empty |
| 3 | 299 | 0.69 | 0.84 | 46 | empty |
| 4 | 406 | 0.67 | 0.80 | 41 | empty |
| 5 | 611 | 0.67 | 0.77 | 53 | empty |
Interfaces
7 interfaces between chains.
- D–F · 1219 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–C · 846 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 811 Ų buried · 18 hydrogen bonds · protein-nucleic
- D–E · 791 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–D · 698 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4DSF · Ternary complex of Bacillus DNA Polymerase I Large Fragment F710Y, DNA duplex, and rCTP… · 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 4DSF · PDBe 4DSF · UniProt Q5KWC1
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