MolNFT v1 · #89584 · protein + DNA
RB69 DNA polymerase ternary complex with dctp opposite an abasic site and DDG/DC as the penultimate base-pair
4DTM: “RB69 DNA polymerase ternary complex with dctp opposite an abasic site and DDG/DC as the penultimate base-pair”. X-ray diffraction, 2 ligands (DCP, CA), 11 pockets (best druggability 0.84). MolNFT v1 #89584 on GenesisL1: 3D…
- PDB
- 4DTM
- 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
- DCP, 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
- 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 | 276 | 0.84 | 0.95 | 33 | empty |
| 2 | 283 | 0.75 | 0.88 | 51 | DCP, CA |
| 3 | 248 | 0.71 | 0.86 | 32 | CA |
| 4 | 173 | 0.64 | 0.85 | 26 | empty |
| 5 | 396 | 0.62 | 0.77 | 45 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1288 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–P · 694 Ų buried · 17 hydrogen bonds · protein-nucleic
- T–P · 616 Ų buried · 58 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4DTM · RB69 DNA Polymerase Ternary Complex with dCTP Opposite an Abasic Site and ddG/dC 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 4DTM · PDBe 4DTM · UniProt Q38087
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