Research workbench
Complex structure of hcmv protease and a peptidomimetic inhibitor
Analyse Complex structure of hcmv protease and a peptidomimetic inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NKM
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Assemblin
- EC
- 3.4.21.97
- UniProt
- P16753
- Ligands
- 0FP
- Pockets
- 8 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Assemblin (EC 3.4.21.97) | protein | 220 | 36% helix, 22% strand | P16753 |
| B | Assemblin (EC 3.4.21.97) | protein | 220 | 36% helix, 20% 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 · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.54 | 0.88 | 16 | empty |
| 2 | 179 | 0.53 | 0.79 | 38 | empty |
| 3 | 123 | 0.42 | 0.76 | 18 | empty |
| 4 | 63 | 0.38 | 0.79 | 14 | empty |
| 5 | 99 | 0.36 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1578 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1NKM · Complex structure of HCMV Protease and a peptidomimetic inhibitor · the same entry in another collection · chain B against B, 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 1NKM · PDBe 1NKM · UniProt P16753
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