MolNFT v1 · #72738 · protein + DNA
RB69 DNA polymerase (S565G/Y567A) ternary complex with dttp opposite dg
3NHG: “RB69 DNA polymerase (S565G/Y567A) ternary complex with dttp opposite dg”. X-ray diffraction, 2 ligands (TTP, CA), 8 pockets (best druggability 0.84). MolNFT v1 #72738 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3NHG
- 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
- TTP, CA
- Pockets
- 8 · best druggability 0.84
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
- TTP · Thymidine-5'-triphosphate · ligand · chains A, T, P
- CA · Calcium ion · metal · 6 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 280 | 0.84 | 0.95 | 33 | empty |
| 2 | 939 | 0.82 | 0.83 | 77 | CA |
| 3 | 340 | 0.72 | 0.85 | 33 | TTP, CA |
| 4 | 463 | 0.64 | 0.77 | 48 | empty |
| 5 | 122 | 0.55 | 0.83 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1367 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–P · 682 Ų buried · 16 hydrogen bonds · protein-nucleic
- T–P · 611 Ų buried · 62 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3NHG · RB69 DNA Polymerase (S565G/Y567A) Ternary Complex with dTTP Opposite dG · 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 3NHG · PDBe 3NHG · UniProt Q38087
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