Research workbench
RB69 DNA polymerase ternary complex with dctp opposite an abasic site and DDA/DT as the penultimate base-pair
Analyse RB69 DNA polymerase ternary complex with dctp 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
- 4DTO
- 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
- DCP, CA
- Pockets
- 11 · 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
- DCP · 2'-deoxycytidine-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
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.83 | 0.93 | 34 | empty |
| 2 | 1193 | 0.78 | 0.80 | 81 | CA |
| 3 | 1107 | 0.78 | 0.80 | 94 | DCP, CA |
| 4 | 560 | 0.66 | 0.77 | 47 | empty |
| 5 | 118 | 0.57 | 0.84 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1055 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–P · 653 Ų buried · 13 hydrogen bonds · protein-nucleic
- T–P · 587 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4DTO · RB69 DNA Polymerase Ternary Complex with dCTP 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 4DTO · PDBe 4DTO · UniProt Q38087
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