MolNFT v1 · #89581 · protein + DNA
RB69 DNA polymerase ternary complex with dttp opposite an abasic site and DDT/DA as the penultimate base-pair
4DTJ: “RB69 DNA polymerase ternary complex with dttp opposite an abasic site and DDT/DA as the penultimate base-pair”. X-ray diffraction, 2 ligands (TTP, CA), 10 pockets (best druggability 0.82). MolNFT v1 #89581 on GenesisL1: 3D…
- PDB
- 4DTJ
- Type
- protein + DNA
- Length
- 932 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
- TTP, CA
- Pockets
- 10 · best druggability 0.82
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 | 901 | 45% helix, 19% strand | Q38087 |
| T | DNA template | dna | 18 | — | — |
| P | DNA primer | dna | 13 | — | — |
Ligands and binding sites
- TTP · Thymidine-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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.82 | 0.94 | 36 | empty |
| 2 | 308 | 0.77 | 0.88 | 52 | TTP, CA |
| 3 | 263 | 0.72 | 0.86 | 31 | CA |
| 4 | 186 | 0.65 | 0.85 | 25 | empty |
| 5 | 419 | 0.62 | 0.77 | 46 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1292 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–P · 670 Ų buried · 16 hydrogen bonds · protein-nucleic
- T–P · 611 Ų buried · 56 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4DTJ · RB69 DNA Polymerase Ternary Complex with dTTP Opposite an Abasic Site and ddT/dA 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 4DTJ · PDBe 4DTJ · UniProt Q38087
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