MolNFT v1 · #137620 · protein + DNA
Tna polymerase, translocated product
5VU9 · DNA polymerase: “Tna polymerase, translocated product”. X-ray diffraction, 1 ligand (FA2), 7 pockets (best druggability 0.79). MolNFT v1 #137620 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VU9
- Type
- protein + DNA
- Length
- 785 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
- Ligands
- FA2
- Pockets
- 7 · best druggability 0.79
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 | 757 | 41% helix, 23% strand | D0VWU9 |
| T | DNA template | dna | 16 | — | — |
| P | DNA/TNA hybrid primer | dna | 12 | — | — |
Ligands and binding sites
- FA2 · 5-(6-amino-9H-purin-9-yl)-4-hydroxytetrahydrofuran-3-yl dihydrogen phosphate · ligand · chains A, T, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.79 | 0.81 | 103 | empty |
| 2 | 214 | 0.75 | 0.91 | 29 | empty |
| 3 | 169 | 0.55 | 0.80 | 22 | empty |
| 4 | 157 | 0.54 | 0.81 | 20 | FA2 |
| 5 | 84 | 0.52 | 0.84 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1160 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–P · 634 Ų buried · 22 hydrogen bonds · protein-nucleic
- T–P · 578 Ų buried · 56 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent, 1 disulfide, 1 modified (covalent ligand, disulfide, nucleotide modification).
Compared structures
- 5VU9 · TNA polymerase, translocated product · the same entry in another collection · chain P against P, 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 5VU9 · PDBe 5VU9 · UniProt D0VWU9
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