7D3C | pdb_00007d3c

The newly emerged SARS-like coronavirus HCoV-EMC also has an "Achilles' heel": current effective inhibitor targeting a 3C-like protease

• PDB DOI: https://doi.org/10.2210/pdb7D3C/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Middle East respiratory syndrome-related coronavirus, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-09-18 Released: 2021-11-03 
• Deposition Author(s): Yan, L., Ren, Z.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.278 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

The newly emerged SARS-like coronavirus HCoV-EMC also has an "Achilles' heel": current effective inhibitor targeting a 3C-like protease

Ren, Z., Yan, L., Zhang, N., Guo, Y., Yang, C., Lou, Z., Rao, Z.

(2013) Protein Cell 4: 248-250

• PubMed: 23549610 
• DOI: https://doi.org/10.1007/s13238-013-2841-3
• Primary Citation Related Structures: 
  7D3C

---

Organizational Affiliation: 
• College of Pharmacy and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 68.07 kDa 
• Atom Count: 4,939 
• Modeled Residue Count: 614 
• Deposited Residue Count: 624 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A [auth B], B [auth A]	306	Middle East respiratory syndrome-related coronavirus	Mutation(s): 0  EC: 3.4.19.12 (PDB Primary Data), 3.4.22.69 (PDB Primary Data)
UniProt
Find proteins for K9N7C7 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)) Explore K9N7C7  Go to UniProtKB:  K9N7C7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE	C, D [auth E]	6	synthetic construct	Mutation(s): 0

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002214	C, D [auth E]	N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.278 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.62	α = 90
b = 93.223	β = 90
c = 103.015	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-11-03 
Deposition Author(s): Yan, L., Ren, Z.

Revision History  

• Version 1.0: 2021-11-03
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2023-11-29
  Changes: Refinement description
• Version 2.2: 2024-10-16
  Changes: Structure summary