MolNFT v1 · #137617 · protein + DNA
Tna polymerase binary complex with PRIMER/TEMPLATE duplex
5VU6 · DNA polymerase: “Tna polymerase binary complex with PRIMER/TEMPLATE duplex”. X-ray diffraction, 7 pockets (best druggability 0.78). MolNFT v1 #137617 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VU6
- Type
- protein + DNA
- Length
- 782 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA template; DNA/TNA hybrid primer
- EC
- 2.7.7.7
- UniProt
- D0VWU9
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 756 | 41% helix, 23% strand | D0VWU9 |
| T | DNA template | dna | 14 | — | — |
| P | DNA/TNA hybrid primer | dna | 12 | — | — |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.78 | 0.92 | 41 | empty |
| 2 | 1153 | 0.77 | 0.79 | 120 | empty |
| 3 | 943 | 0.75 | 0.78 | 69 | empty |
| 4 | 216 | 0.54 | 0.78 | 30 | empty |
| 5 | 101 | 0.40 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1124 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–P · 733 Ų buried · 24 hydrogen bonds · protein-nucleic
- T–P · 563 Ų buried · 60 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 disulfide, 1 isopeptide, 1 modified (disulfide, isopeptide, nucleotide modification).
Compared structures
- 5VU6 · TNA polymerase binary complex with primer/template duplex · 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 D0VWU9
- Elsewhere: RCSB PDB 5VU6 · PDBe 5VU6 · UniProt D0VWU9
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