Research workbench
Crystal structure of RB69 GP43 with DNA and datp opposite 8-oxog
Analyse Crystal structure of RB69 GP43 with DNA and datp opposite 8-oxog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LDS
- Type
- protein + DNA
- Length
- 935 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed DNA polymerase; DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*(DDG))…
- EC
- 2.7.7.7, 3.1.11.-
- UniProt
- Q38087
- Ligands
- DTP, MN, SO4
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed DNA polymerase (EC 2.7.7.7, 3.1.11.-) | protein | 903 | 44% helix, 19% strand | Q38087 |
| P | DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*(DDG))- 3') | dna | 14 | — | — |
| T | DNA (5'-D(*CP*AP*(8OG) P*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3') | dna | 18 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, P, T
- MN · Manganese (II) ion · metal · 3 copies · chains A, P
- SO4 · Sulfate ion · ion · 2 copies · chains P, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.82 | 0.93 | 33 | empty |
| 2 | 648 | 0.78 | 0.83 | 77 | MN |
| 3 | 612 | 0.76 | 0.82 | 55 | DTP, MN |
| 4 | 354 | 0.64 | 0.79 | 38 | empty |
| 5 | 132 | 0.58 | 0.84 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1200 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–P · 709 Ų buried · 14 hydrogen bonds · protein-nucleic
- P–T · 642 Ų buried · 63 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3LDS · Crystal structure of RB69 gp43 with DNA and dATP opposite 8-oxoG · 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 Q38087
- Elsewhere: RCSB PDB 3LDS · PDBe 3LDS · UniProt Q38087
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