MolNFT v1 · #186864 · protein + DNA
Tna polymerase, N+2 product
7RSU · DNA polymerase: “Tna polymerase, N+2 product”. X-ray diffraction, 2 ligands (TFT, FA2), 8 pockets (best druggability 0.80). MolNFT v1 #186864 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7RSU
- Type
- protein + DNA
- Length
- 781 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; Template; Primer
- EC
- 2.7.7.7
- UniProt
- D0VWU9
- Ligands
- TFT, FA2
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 756 | 43% helix, 23% strand | D0VWU9 |
| T | Template | dna | 14 | — | — |
| P | Primer | dna | 11 | — | — |
Ligands and binding sites
- TFT · (L)-alpha-threofuranosyl-thymine-3'-monophosphate · ligand · chains A, T, P
- FA2 · 5-(6-amino-9H-purin-9-yl)-4-hydroxytetrahydrofuran-3-yl dihydrogen phosphate · ligand · chains A, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.80 | 0.82 | 61 | empty |
| 2 | 210 | 0.76 | 0.91 | 38 | empty |
| 3 | 353 | 0.58 | 0.76 | 45 | TFT, FA2 |
| 4 | 209 | 0.54 | 0.78 | 27 | empty |
| 5 | 105 | 0.50 | 0.82 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–T · 968 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–P · 558 Ų buried · 18 hydrogen bonds · protein-nucleic
- T–P · 544 Ų buried · 57 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7RSU · TNA polymerase, n+2 product · the same entry in another collection · chain T against T, 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 7RSU · PDBe 7RSU · UniProt D0VWU9
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