MolNFT v1 · #177442 · protein
SARS-cov-2 main proteinase complex with microbial metabolite leupeptin
7EIN · 3C-like proteinase: “SARS-cov-2 main proteinase complex with microbial metabolite leupeptin”. X-ray diffraction, 1 ligand (OAR), 5 pockets (best druggability 0.76). MolNFT v1 #177442 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7EIN
- Type
- protein
- Length
- 604 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; Leupeptin
- EC
- 3.4.22.69
- UniProt
- P0DTC1
- Ligands
- OAR
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.69) | protein | 300 | 26% helix, 29% strand | P0DTC1 |
| C, D | Leupeptin | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- OAR · N-(4-amino-5-hydroxy-pentyl)-guanidine · ligand · 2 copies · chains A, C, B, D
- ACY · Acetic acid · additive · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.76 | 0.78 | 88 | empty |
| 2 | 160 | 0.54 | 0.80 | 38 | empty |
| 3 | 86 | 0.42 | 0.79 | 19 | OAR |
| 4 | 114 | 0.37 | 0.74 | 27 | empty |
| 5 | 56 | 0.27 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1290 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 272 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 270 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand, additive adduct).
Compared structures
- 7EIN · SARS-CoV-2 main proteinase complex with microbial metabolite leupeptin · 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 P0DTC1
- Elsewhere: RCSB PDB 7EIN · PDBe 7EIN · UniProt P0DTC1
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