MolNFT v1 · #75602 · protein + DNA
Crystal structure of bacillus DNA polymerase I large fragment bound to DNA and ddttp-da in closed conformation
3PV8: “Crystal structure of bacillus DNA polymerase I large fragment bound to DNA and ddttp-da in closed conformation”. X-ray diffraction, 3 ligands (D3T, MG, SO4), 18 pockets (best druggability 0.77). MolNFT v1 #75602 on GenesisL1: 3D…
- PDB
- 3PV8
- 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; DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q5KWC1
- Ligands
- D3T, MG, SO4
- Pockets
- 18 · best druggability 0.77
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 | Q5KWC1 |
| B, E | DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3') | dna | 9 | — | — |
| C, F | DNA (5'-D(*C*AP*TP*AP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- D3T · 2',3'-dideoxy-thymidine-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 · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.77 | 0.79 | 73 | MG, D3T, SO4 |
| 2 | 939 | 0.77 | 0.79 | 68 | MG, D3T |
| 3 | 715 | 0.73 | 0.79 | 57 | empty |
| 4 | 335 | 0.68 | 0.82 | 44 | empty |
| 5 | 520 | 0.67 | 0.78 | 49 | empty |
Interfaces
7 interfaces between chains.
- D–F · 1215 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 1207 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 767 Ų buried · 21 hydrogen bonds · protein-nucleic
- D–E · 766 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–D · 572 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3PV8 · Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddTTP-dA… · 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 Q5KWC1
- Elsewhere: RCSB PDB 3PV8 · PDBe 3PV8 · UniProt Q5KWC1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.