MolNFT v1 · #79144 · protein + DNA
RB69 DNA polymerase (Y567A) ternary complex with dttp opposite 2AP (at rich sequence)
3SUN: “RB69 DNA polymerase (Y567A) ternary complex with dttp opposite 2AP (at rich sequence)”. X-ray diffraction, 2 ligands (TTP, CA), 12 pockets (best druggability 0.84). MolNFT v1 #79144 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3SUN
- Type
- protein + DNA
- Length
- 924 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; 5'-D(P*CP*(2PR)P*TP*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*G)- 3'…
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- TTP, CA
- Pockets
- 12 · 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 | 895 | 44% helix, 19% strand | Q38087 |
| T | 5'-D(P*CP*(2PR)P*TP*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*G)- 3' | dna | 16 | — | — |
| P | 5'-D(*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*(2DA))-3' | 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
12 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 | 26 | empty |
| 2 | 1088 | 0.78 | 0.80 | 75 | CA |
| 3 | 1135 | 0.77 | 0.79 | 101 | TTP, CA |
| 4 | 138 | 0.58 | 0.83 | 21 | empty |
| 5 | 245 | 0.51 | 0.75 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1100 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–P · 722 Ų buried · 17 hydrogen bonds · protein-nucleic
- T–P · 546 Ų buried · 44 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3SUN · RB69 DNA Polymerase (Y567A) Ternary Complex with dTTP Opposite 2AP (AT rich sequence) · 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 3SUN · PDBe 3SUN · UniProt Q38087
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