MolNFT v1 · #108927 · protein
Crystal structure of catalytically inactive MERS-cov 3CL protease (C148A) in spacegroup P212121
4WMF: “Crystal structure of catalytically inactive MERS-cov 3CL protease (C148A) in spacegroup P212121”. X-ray diffraction, 8 pockets (best druggability 0.78). MolNFT v1 #108927 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4WMF
- Type
- protein
- Length
- 896 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MERS-cov 3CL protease
- UniProt
- W6A941
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MERS-cov 3CL protease | protein | 304 | 26% helix, 30% strand | W6A941 |
| B | MERS-cov 3CL protease | protein | 303 | 25% helix, 30% strand | W6A941 |
| C | MERS-cov 3CL protease | protein | 289 | 25% helix, 32% strand | W6A941 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · 5 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.78 | 0.80 | 86 | PEG |
| 2 | 612 | 0.67 | 0.76 | 71 | PG4 |
| 3 | 430 | 0.63 | 0.77 | 53 | PG4 |
| 4 | 212 | 0.54 | 0.78 | 27 | PG4 |
| 5 | 219 | 0.53 | 0.77 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1336 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 719 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4WMF · Crystal structure of catalytically inactive MERS-CoV 3CL protease (C148A) in spacegroup… · 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 W6A941
- Elsewhere: RCSB PDB 4WMF · PDBe 4WMF · UniProt W6A941
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