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
- 1NKK
- Type
- protein
- Length
- 910 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein P40; Peptidomimetic inhibitor
- EC
- 3.4.21.97
- UniProt
- P16753
- Ligands
- ACE, CFT
- Pockets
- 14 · best druggability 0.56
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein P40 (EC 3.4.21.97) | protein | 222 | 36% helix, 25% strand | P16753 |
| B | Capsid protein P40 (EC 3.4.21.97) | protein | 226 | 35% helix, 23% strand | P16753 |
| C | Capsid protein P40 (EC 3.4.21.97) | protein | 226 | 36% helix, 23% strand | P16753 |
| D | Capsid protein P40 (EC 3.4.21.97) | protein | 220 | 35% helix, 25% strand | P16753 |
| E, F, G, H | Peptidomimetic inhibitor | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- CFT · Trifluoromethane · ligand · 4 copies · chains A, E, B, F, C, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.56 | 0.79 | 42 | CFT |
| 2 | 102 | 0.53 | 0.83 | 20 | empty |
| 3 | 82 | 0.53 | 0.85 | 18 | empty |
| 4 | 219 | 0.52 | 0.77 | 45 | CFT |
| 5 | 218 | 0.50 | 0.76 | 38 | CFT |
Interfaces
7 interfaces between chains.
- C–D · 1515 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1515 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 478 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 423 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 406 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 8 modified (covalent ligand, nonstandard).
Compared structures
- 1NKK · 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 1NKK · PDBe 1NKK · UniProt P16753
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