Research workbench
DNA polymerase I large fragment from bacillus stearothermophilus with DNA template and 3'-amino primer
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
- 6UR4
- Type
- protein + DNA
- Length
- 599 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))-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- D9N168
- Pockets
- 8 · best druggability 0.70
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))-3') | dna | 9 | — | — |
| C | DNA (5'-D(P*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3') | dna | 11 | — | — |
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 | 816 | 0.70 | 0.76 | 67 | empty |
| 2 | 106 | 0.69 | 0.93 | 17 | empty |
| 3 | 315 | 0.69 | 0.83 | 45 | empty |
| 4 | 162 | 0.49 | 0.78 | 19 | empty |
| 5 | 150 | 0.48 | 0.77 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1086 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–B · 683 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–C · 434 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6UR4 · 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 6UR4 · PDBe 6UR4 · UniProt D9N168
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