Research workbench
Ternary complex of bacillus DNA polymerase I large fragment F710Y, DNA duplex, and rctp (paired with dg of template) in presence of MG2+
Analyse Ternary complex of bacillus DNA polymerase I large fragment F710Y, DNA duplex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DSE
- 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 | 52% helix, 15% strand | Q5KWC1 |
| D | DNA polymerase (EC 2.7.7.7) | protein | 579 | 54% helix, 13% 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 | 866 | 0.75 | 0.79 | 69 | CTP |
| 2 | 705 | 0.73 | 0.79 | 54 | empty |
| 3 | 489 | 0.70 | 0.80 | 46 | empty |
| 4 | 292 | 0.69 | 0.84 | 44 | empty |
| 5 | 217 | 0.67 | 0.85 | 31 | empty |
Interfaces
7 interfaces between chains.
- D–F · 1215 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 841 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–B · 818 Ų buried · 19 hydrogen bonds · protein-nucleic
- D–E · 785 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–D · 681 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4DSE · 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 4DSE · PDBe 4DSE · UniProt Q5KWC1
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