MolNFT v1 · #108925 · protein
Crystal structure of catalytically inactive MERS-cov 3CL protease (C148A) in spacegroup C2221
4WMD · ORF1A: “Crystal structure of catalytically inactive MERS-cov 3CL protease (C148A) in spacegroup C2221”. X-ray diffraction, 8 pockets (best druggability 0.77). MolNFT v1 #108925 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4WMD
- Type
- protein
- Length
- 908 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF1A
- UniProt
- W6A941
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ORF1A | protein | 301 | 24% helix, 28% strand | W6A941 |
| B | ORF1A | protein | 304 | 25% helix, 29% strand | W6A941 |
| C | ORF1A | protein | 303 | 24% helix, 29% strand | W6A941 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, C
- PGE · Triethylene glycol · additive · 2 copies · chains A, C
- PG4 · Tetraethylene glycol · additive · chains A, B
- 1PE · Pentaethylene glycol · additive · chains 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.77 | 0.79 | 61 | PEG |
| 2 | 665 | 0.66 | 0.75 | 86 | PG4 |
| 3 | 299 | 0.55 | 0.76 | 36 | empty |
| 4 | 184 | 0.52 | 0.78 | 25 | PGE |
| 5 | 230 | 0.52 | 0.76 | 28 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1322 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 309 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4WMD · 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 4WMD · PDBe 4WMD · UniProt W6A941
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