MolNFT v1 · #181421 · protein + DNA
HSV1 polymerase ternary complex with dsdna and pnu-183792
7LUF · DNA polymerase: “HSV1 polymerase ternary complex with dsdna and pnu-183792”. X-ray diffraction, 1 ligand (YE4), 20 pockets (best druggability 0.80). MolNFT v1 #181421 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7LUF
- Type
- protein + DNA
- Length
- 2,164 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA (5'- D(P*AP*TP*GP*GP*TP*AP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*CP*G)-3')…
- EC
- 2.7.7.7
- UniProt
- I7GY94
- Ligands
- YE4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 1044 | 39% helix, 21% strand | I7GY94 |
| C, E | DNA (5'- D(P*AP*TP*GP*GP*TP*AP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*CP*G)-3') | dna | 18 | — | — |
| D, F | DNA (5'-D(*CP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)- 3') | dna | 15 | — | — |
| B | DNA polymerase (EC 2.7.7.7) | protein | 1054 | 39% helix, 21% strand | I7GY94 |
Ligands and binding sites
- YE4 · N-(4-chlorobenzyl)-1-methyl-6-(morpholinomethyl)-4-oxo-1,4-dihydroquinoline-3-carboxamide · ligand · 2 copies · chains A, C, D, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.80 | 0.81 | 83 | empty |
| 2 | 447 | 0.80 | 0.88 | 65 | empty |
| 3 | 607 | 0.79 | 0.85 | 70 | empty |
| 4 | 1152 | 0.77 | 0.79 | 90 | empty |
| 5 | 1037 | 0.76 | 0.79 | 81 | YE4 |
Interfaces
7 interfaces between chains.
- B–E · 1384 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–B · 1265 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1223 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–F · 777 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–D · 724 Ų buried · 24 hydrogen bonds · protein-nucleic
Compared structures
- 7LUF · HSV1 polymerase ternary complex with dsDNA and PNU-183792 · 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 I7GY94
- Elsewhere: RCSB PDB 7LUF · PDBe 7LUF · UniProt I7GY94
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