Research workbench
DNA polymerase I large fragment from bacillus stearothermophilus with DNA template, dideoxy primer, 3'-amino-ddgtp (ngtp), and CA2+
Analyse DNA polymerase I large fragment from bacillus stearothermophilus with DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UR9
- Type
- protein + DNA
- Length
- 1,199 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I; DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*(DOC))-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- D9N168
- Ligands
- NG3, CA, SO4
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA polymerase I (EC 2.7.7.7) | protein | 579 | 55% helix, 13% strand | D9N168 |
| B, E | DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*(DOC))-3') | dna | 9 | — | — |
| C | DNA (5'-D(*CP*AP*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3') | dna | 11 | — | — |
| F | DNA (5'-D(*CP*AP*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3') | dna | 12 | — | — |
Ligands and binding sites
- NG3 · 3'-amino-2',3'-dideoxyguanosine 5'-(tetrahydrogen triphosphate) · ligand · chains A, B, C
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 9 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.77 | 0.80 | 72 | NG3, CA |
| 2 | 874 | 0.74 | 0.78 | 80 | empty |
| 3 | 325 | 0.73 | 0.86 | 36 | empty |
| 4 | 146 | 0.70 | 0.90 | 22 | empty |
| 5 | 388 | 0.69 | 0.81 | 43 | SO4 |
Interfaces
12 interfaces between chains.
- D–F · 1249 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 1141 Ų buried · 20 hydrogen bonds · protein-nucleic
- D–E · 766 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 728 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–D · 525 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6UR9 · DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template… · the same entry in another collection · chain F against F, 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 D9N168
- Elsewhere: RCSB PDB 6UR9 · PDBe 6UR9 · UniProt D9N168
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