Research workbench
Bacillus fragment DNA polymerase mutant I716M
Analyse Bacillus fragment DNA polymerase mutant I716M in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P5C
- Type
- protein + DNA
- Length
- 599 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*C)-3'); DNA (5'-D(P*GP*CP*GP*TP*GP*AP*TP*CP*G)-3')…
- EC
- 2.7.7.7
- UniProt
- D9N168
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*C)-3') | dna | 9 | — | — |
| C | DNA (5'-D(P*GP*CP*GP*TP*GP*AP*TP*CP*G)-3') | dna | 9 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 581 | 55% helix, 13% strand | D9N168 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.73 | 0.92 | 23 | empty |
| 2 | 358 | 0.70 | 0.82 | 42 | empty |
| 3 | 310 | 0.60 | 0.78 | 35 | SO4 |
| 4 | 151 | 0.46 | 0.77 | 28 | empty |
| 5 | 55 | 0.46 | 0.85 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–A · 862 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–A · 773 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–C · 424 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Compared structures
- 6P5C · Bacillus Fragment DNA polymerase mutant I716M · the same entry in another collection · chain B against B, 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 6P5C · PDBe 6P5C · UniProt D9N168
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