Research workbench
Crystal structure of bacillus DNA polymerase I large fragment bound to DNA and ddctp-da mismatch (tautomer) in closed conformation
Analyse Crystal structure of bacillus DNA polymerase I large fragment bound to DNA and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PX6
- Type
- protein + DNA
- Length
- 1,202 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I; DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q5KWC1
- Ligands
- DCT, MN, SO4
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I (EC 2.7.7.7) | protein | 579 | 54% helix, 13% strand | Q5KWC1 |
| D | DNA polymerase I (EC 2.7.7.7) | protein | 581 | 55% helix, 13% strand | Q5KWC1 |
| B, E | DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3') | dna | 9 | — | — |
| C, F | DNA (5'-D(*C*AP*TP*AP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · 3 copies · chains A, B, C, D, E, F
- MN · Manganese (II) ion · metal · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.77 | 0.80 | 75 | DCT, MN |
| 2 | 980 | 0.76 | 0.79 | 69 | DCT, MN |
| 3 | 665 | 0.73 | 0.79 | 50 | SO4 |
| 4 | 593 | 0.69 | 0.78 | 51 | empty |
| 5 | 227 | 0.68 | 0.85 | 29 | empty |
Interfaces
7 interfaces between chains.
- A–C · 1237 Ų buried · 22 hydrogen bonds · protein-nucleic
- D–F · 1236 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–B · 801 Ų buried · 23 hydrogen bonds · protein-nucleic
- D–E · 760 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–D · 625 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3PX6 · Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddCTP-dA… · 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 3PX6 · PDBe 3PX6 · UniProt Q5KWC1
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