Research workbench
RB69 DNA polymerase ternary complex with datp opposite an abasic site and DDA/DT as the penultimate base-pair
Analyse RB69 DNA polymerase ternary complex with datp opposite an abasic site and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DTN
- Type
- protein + DNA
- Length
- 933 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA template; DNA primer
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- DTP, CA
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 903 | 45% helix, 19% strand | Q38087 |
| T | DNA template | dna | 17 | — | — |
| P | DNA primer | dna | 13 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, T, P
- CA · Calcium ion · metal · 5 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.83 | 0.93 | 37 | empty |
| 2 | 1190 | 0.79 | 0.80 | 91 | CA |
| 3 | 1146 | 0.77 | 0.79 | 100 | DTP, CA |
| 4 | 551 | 0.66 | 0.77 | 54 | empty |
| 5 | 124 | 0.54 | 0.82 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1096 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–P · 661 Ų buried · 16 hydrogen bonds · protein-nucleic
- T–P · 590 Ų buried · 56 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4DTN · RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddA/dT as the… · 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 4DTN · PDBe 4DTN · UniProt Q38087
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