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
- 1NJT
- Type
- protein
- Length
- 914 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, CL
- Pockets
- 11 · best druggability 0.55
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein P40 (EC 3.4.21.97) | protein | 226 | 38% helix, 23% strand | P16753 |
| B | Capsid protein P40 (EC 3.4.21.97) | protein | 227 | 40% helix, 22% strand | P16753 |
| C | Capsid protein P40 (EC 3.4.21.97) | protein | 222 | 38% helix, 22% strand | P16753 |
| D | Capsid protein P40 (EC 3.4.21.97) | protein | 223 | 37% helix, 23% 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
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.55 | 0.86 | 20 | empty |
| 2 | 75 | 0.54 | 0.86 | 18 | empty |
| 3 | 220 | 0.54 | 0.78 | 41 | CFT, CL |
| 4 | 190 | 0.53 | 0.78 | 37 | CFT, CL |
| 5 | 181 | 0.50 | 0.77 | 31 | CFT, CL |
Interfaces
7 interfaces between chains.
- C–D · 1610 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1593 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 422 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 416 Ų buried · 12 hydrogen bonds · protein-protein
- C–G · 412 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 8 modified (covalent ligand, nonstandard).
Compared structures
- 1NJT · 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 1NJT · PDBe 1NJT · UniProt P16753
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