MolNFT v1 · #15936 · protein
Complex structure of hcmv protease and a peptidomimetic inhibitor
1NJU · Assemblin: “Complex structure of hcmv protease and a peptidomimetic inhibitor”. X-ray diffraction, 1 ligand (0FP), 14 pockets (best druggability 0.60). MolNFT v1 #15936 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1NJU
- Type
- protein
- Length
- 917 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Assemblin
- EC
- 3.4.21.97
- UniProt
- P16753
- Ligands
- 0FP
- Pockets
- 14 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Assemblin (EC 3.4.21.97) | protein | 230 | 35% helix, 22% strand | P16753 |
| B | Assemblin (EC 3.4.21.97) | protein | 230 | 35% helix, 22% strand | P16753 |
| C | Assemblin (EC 3.4.21.97) | protein | 227 | 34% helix, 23% strand | P16753 |
Ligands and binding sites
- 0FP · N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~1~-[(2S,3S)-3-hydroxy-4-oxo-4-{[(1R)-1-phenylpropyl]amino}butan-2-yl]-N~4~,N~4~-dimethyl-L-aspartamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.60 | 0.83 | 38 | empty |
| 2 | 244 | 0.58 | 0.79 | 28 | empty |
| 3 | 83 | 0.54 | 0.86 | 18 | empty |
| 4 | 157 | 0.53 | 0.80 | 44 | 0FP |
| 5 | 119 | 0.48 | 0.79 | 31 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1605 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1589 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 381 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1NJU · Complex structure of HCMV Protease and a peptidomimetic inhibitor · 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 P16753
- Elsewhere: RCSB PDB 1NJU · PDBe 1NJU · UniProt P16753
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