MolNFT v1 · #89338 · protein
X-ray structure of human hepatitus C virus NS5A-transactivated protein 2 at the resolution 1.9A, northeast structural genomics consortium (nesg) target HR6723
4DMB · Hd domain-containing protein 2: “X-ray structure of human hepatitus C virus NS5A-transactivated protein 2 at the resolution 1.9A, northeast…”. X-ray diffraction, 4 ligands (UNL, MG, NO3), 4 pockets (best druggability 0.64). MolNFT…
- PDB
- 4DMB
- Type
- protein
- Length
- 378 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hd domain-containing protein 2
- UniProt
- Q7Z4H3
- Ligands
- UNL, MG, NO3, PO4
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hd domain-containing protein 2 | protein | 188 | 73% helix, 1% strand | Q7Z4H3 |
| B | Hd domain-containing protein 2 | protein | 190 | 73% helix, 1% strand | Q7Z4H3 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · chains B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- NO3 · Nitrate ion · ion · 3 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.64 | 0.78 | 34 | MG, PO4 |
| 2 | 396 | 0.63 | 0.78 | 33 | UNL, MG |
| 3 | 227 | 0.53 | 0.77 | 33 | GOL |
| 4 | 52 | 0.34 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2336 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 4DMB · X-ray structure of human hepatitus C virus NS5A-transactivated protein 2 at the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7Z4H3 · AlphaFold monomer V2.0 prediction for 5'-deoxynucleotidase HDDC2 (Q7Z4H3) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q7Z4H3
- Elsewhere: RCSB PDB 4DMB · PDBe 4DMB · UniProt Q7Z4H3
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