Research workbench
Crystal structure of MERS main protease in complex with PF07321332
Analyse Crystal structure of MERS main protease in complex with PF07321332 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VTC
- Type
- protein
- Length
- 600 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.19.12, 3.4.22.69
- UniProt
- T2B9A8
- Ligands
- 4WI
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.19.12, 3.4.22.69) | protein | 299 | 23% helix, 29% strand | T2B9A8 |
| B | 3C-like proteinase (EC 3.4.19.12, 3.4.22.69) | protein | 301 | 25% helix, 27% strand | T2B9A8 |
Ligands and binding sites
- 4WI · (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.74 | 0.77 | 78 | empty |
| 2 | 306 | 0.57 | 0.77 | 49 | empty |
| 3 | 261 | 0.55 | 0.77 | 37 | empty |
| 4 | 237 | 0.53 | 0.76 | 28 | empty |
| 5 | 263 | 0.50 | 0.74 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 931 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7VTC · Crystal structure of MERS main protease in complex with PF07321332 · 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 T2B9A8
- Elsewhere: RCSB PDB 7VTC · PDBe 7VTC · UniProt T2B9A8
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