MolNFT v1 · #38373 · protein
Crystal structure of the herpes simplex virus type 1 DNA polymerase
2GV9: “Crystal structure of the herpes simplex virus type 1 DNA polymerase”. X-ray diffraction, 3 ligands (GAI, HG, SO4), 20 pockets (best druggability 0.72). MolNFT v1 #38373 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2GV9
- Type
- protein
- Length
- 2,016 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase
- EC
- 2.7.7.7
- UniProt
- P04292
- Ligands
- GAI, HG, SO4
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 981 | 38% helix, 23% strand | P04292 |
| B | DNA polymerase (EC 2.7.7.7) | protein | 1035 | 39% helix, 21% strand | P04292 |
Ligands and binding sites
- GAI · Guanidine · ligand · chains B
- HG · Mercury (II) ion · metal · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.72 | 0.82 | 42 | empty |
| 2 | 379 | 0.66 | 0.79 | 39 | empty |
| 3 | 464 | 0.65 | 0.77 | 45 | empty |
| 4 | 364 | 0.59 | 0.76 | 52 | empty |
| 5 | 340 | 0.57 | 0.76 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 720 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2GV9 · Crystal structure of the Herpes Simplex virus type 1 DNA polymerase · 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 P04292
- Elsewhere: RCSB PDB 2GV9 · PDBe 2GV9 · UniProt P04292
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