MolNFT v1 · #108926 · protein
Crystal structure of catalytically inactive MERS-cov 3CL protease (C148A) in spacegroup C2
4WME: “Crystal structure of catalytically inactive MERS-cov 3CL protease (C148A) in spacegroup C2”. X-ray diffraction, 12 pockets (best druggability 0.81). MolNFT v1 #108926 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4WME
- Type
- protein
- Length
- 1,218 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MERS-cov 3CL protease
- UniProt
- W6A941
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | MERS-cov 3CL protease | protein | 306 | 25% helix, 29% strand | W6A941 |
| B | MERS-cov 3CL protease | protein | 304 | 25% helix, 29% strand | W6A941 |
| C | MERS-cov 3CL protease | protein | 302 | 25% helix, 30% strand | W6A941 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.81 | 0.84 | 90 | EDO |
| 2 | 622 | 0.79 | 0.84 | 55 | EDO |
| 3 | 982 | 0.78 | 0.80 | 61 | EDO |
| 4 | 651 | 0.73 | 0.80 | 88 | empty |
| 5 | 592 | 0.68 | 0.77 | 52 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1400 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1389 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 586 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 491 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 462 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4WME · Crystal structure of catalytically inactive MERS-CoV 3CL Protease (C148A) in spacegroup C2 · 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 4WME · PDBe 4WME · UniProt W6A941
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