MolNFT v1 · #24317 · protein
Single stranded DNA-binding PROTEIN(ICP8) from herpes simplex virus-1
1URJ · Major DNA-binding protein: “Single stranded DNA-binding PROTEIN(ICP8) from herpes simplex virus-1”. X-ray diffraction, 2 ligands (HG, ZN), 20 pockets (best druggability 0.84). MolNFT v1 #24317 on GenesisL1: 3D structure, binding…
- PDB
- 1URJ
- Type
- protein
- Length
- 2,058 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major DNA-binding protein
- UniProt
- P04296
- Ligands
- HG, ZN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major DNA-binding protein | protein | 1028 | 38% helix, 17% strand | P04296 |
| B | Major DNA-binding protein | protein | 1030 | 38% helix, 18% strand | P04296 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 8 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.84 | 0.96 | 38 | empty |
| 2 | 227 | 0.83 | 0.96 | 33 | empty |
| 3 | 1065 | 0.79 | 0.80 | 108 | HG |
| 4 | 383 | 0.76 | 0.86 | 42 | empty |
| 5 | 348 | 0.63 | 0.79 | 56 | HG |
Interfaces
1 interface between chains.
- A–B · 1566 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1URJ · Single stranded DNA-binding protein(ICP8) from Herpes simplex virus-1 · 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 P04296
- Elsewhere: RCSB PDB 1URJ · PDBe 1URJ · UniProt P04296
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