Research workbench
Binary complex of bacillus DNA polymerase I large fragment and duplex DNA with rc in primer terminus paired with dg of template
Analyse Binary complex of bacillus DNA polymerase I large fragment and duplex DNA with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DQS
- Type
- protein + DNA
- Length
- 596 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA/RNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-R(P*C)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q5KWC1
- Ligands
- CTP, SO4
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 57% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 573 | 57% helix, 13% strand | Q5KWC1 |
| B | DNA/RNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-R(P*C)-3') | dna | 11 | — | — |
| C | DNA (5'-D(*GP*A*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)- 3') | dna | 12 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.71 | 0.87 | 28 | empty |
| 2 | 355 | 0.69 | 0.82 | 44 | empty |
| 3 | 574 | 0.66 | 0.77 | 57 | SO4 |
| 4 | 120 | 0.48 | 0.79 | 20 | empty |
| 5 | 114 | 0.47 | 0.79 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1068 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–B · 785 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–C · 508 Ų buried · 45 hydrogen bonds · nucleic-nucleic
Compared structures
- 4DQS · Binary complex of Bacillus DNA Polymerase I Large Fragment and duplex DNA with rC in… · 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 4DQS · PDBe 4DQS · UniProt Q5KWC1
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