MolNFT v1 · #72568 · protein + DNA
RB69 DNA polymerase ternary complex with dctp opposite dg at 1.8 ångström resolution
3NCI: “RB69 DNA polymerase ternary complex with dctp opposite dg at 1.8 ångström resolution”. X-ray diffraction, 2 ligands (DCP, CA), 13 pockets (best druggability 0.83). MolNFT v1 #72568 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3NCI
- Type
- protein + DNA
- Length
- 934 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA (5'- D(*TP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')…
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- DCP, CA
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 903 | 43% helix, 19% strand | Q38087 |
| T | DNA (5'- D(*TP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') | dna | 18 | — | — |
| P | DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3') | dna | 13 | — | — |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains A, T, P
- CA · Calcium ion · metal · 3 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.83 | 0.93 | 39 | empty |
| 2 | 843 | 0.81 | 0.84 | 73 | empty |
| 3 | 589 | 0.76 | 0.82 | 51 | DCP, CA |
| 4 | 432 | 0.63 | 0.77 | 43 | empty |
| 5 | 116 | 0.58 | 0.85 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1371 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–P · 679 Ų buried · 16 hydrogen bonds · protein-nucleic
- T–P · 614 Ų buried · 59 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3NCI · RB69 DNA Polymerase Ternary Complex with dCTP Opposite dG at 1.8 angstrom resolution · 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 3NCI · PDBe 3NCI · UniProt Q38087
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.