Research workbench
Crystal structure of bacillus DNA polymerase I large fragment bound to DNA and ddgtp-dc 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
- 3TI0
- Type
- protein + DNA
- Length
- 1,200 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I; 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'…
- EC
- 2.7.7.7
- UniProt
- C9RTX7
- Ligands
- DG3, MG, SO4
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 3 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 | C9RTX7 |
| B, E | 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3' | dna | 9 | — | — |
| C, F | 5'-D(*C*AP*TP*CP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3' | dna | 12 | — | — |
Ligands and binding sites
- DG3 · 2'-3'-dideoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.78 | 0.80 | 73 | DG3, MG |
| 2 | 916 | 0.77 | 0.80 | 69 | DG3, MG |
| 3 | 691 | 0.73 | 0.79 | 56 | empty |
| 4 | 330 | 0.68 | 0.82 | 45 | empty |
| 5 | 341 | 0.66 | 0.81 | 44 | empty |
Interfaces
7 interfaces between chains.
- A–C · 1216 Ų buried · 25 hydrogen bonds · protein-nucleic
- D–F · 1214 Ų buried · 26 hydrogen bonds · protein-nucleic
- D–E · 830 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–B · 823 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–D · 575 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3TI0 · Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddGTP-dC… · 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 C9RTX7
- Elsewhere: RCSB PDB 3TI0 · PDBe 3TI0 · UniProt C9RTX7
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