MolNFT v1 · #89597 · protein + DNA
RB69 DNA polymerase ternary complex with datp opposite dt
4DU1: “RB69 DNA polymerase ternary complex with datp opposite dt”. X-ray diffraction, 2 ligands (DTP, CA), 11 pockets (best druggability 0.84). MolNFT v1 #89597 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4DU1
- 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
- DTP, CA
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 901 | 44% helix, 19% strand | Q38087 |
| T | DNA template | dna | 18 | — | — |
| P | DNA primer | dna | 13 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, T, P
- CA · Calcium ion · metal · 7 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.84 | 0.95 | 33 | empty |
| 2 | 259 | 0.74 | 0.88 | 37 | DTP, CA |
| 3 | 273 | 0.72 | 0.86 | 28 | CA |
| 4 | 245 | 0.70 | 0.86 | 33 | empty |
| 5 | 451 | 0.63 | 0.77 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1368 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–P · 699 Ų buried · 14 hydrogen bonds · protein-nucleic
- T–P · 608 Ų buried · 62 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4DU1 · RB69 DNA Polymerase Ternary Complex with dATP Opposite dT · 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 4DU1 · PDBe 4DU1 · UniProt Q38087
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