Research workbench
DNA polymerase I large fragment from bacillus stearothermophilus with DNA template and primer containing an N3'-> P5' linkage
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
- 6UR2
- Type
- protein + DNA
- Length
- 601 residues
- Chains
- 3
- 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*(C42)P*G)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- D9N168
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I (EC 2.7.7.7) | protein | 579 | 56% helix, 13% strand | D9N168 |
| B | DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*(C42)P*G)-3') | dna | 10 | — | — |
| C | DNA (5'-D(P*AP*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3') | dna | 12 | — | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.71 | 0.76 | 75 | empty |
| 2 | 324 | 0.68 | 0.82 | 45 | empty |
| 3 | 131 | 0.65 | 0.88 | 20 | empty |
| 4 | 137 | 0.44 | 0.76 | 24 | empty |
| 5 | 145 | 0.43 | 0.75 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1066 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–B · 798 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 501 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6UR2 · DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template and… · 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 D9N168
- Elsewhere: RCSB PDB 6UR2 · PDBe 6UR2 · UniProt D9N168
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