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9zjc

Crystal structure of MERS 3CL protease in complex with inhibitor IKR-I-52

Method: X-RAY DIFFRACTION D_max: 76.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zjc
deposition_date	2025-12-04
last_revision	2026-06-10
title	Crystal structure of MERS 3CL protease in complex with inhibitor IKR-I-52
keywords	HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	22.17 Å
rg_electron	21.70 Å
i0	36150100.00
molecular_weight	31097.0 kDa
excluded_volume	30074 Å³
envelope_volume	48818 Å³
shell_volume	19673 Å³
envelope_diameter	76.2 Å
shell_rg	27.30 Å
envelope_rg	21.81 Å
shape_rg	21.72 Å
total_rg	22.22 Å
total_atoms	2336
n_residues	307
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	76.4 Å
rg_real	22.29 Å
rg_real_error	0.58 Å
i0_real	3.6150e+07
i0_real_error	4.9600e+05
rg_reciprocal	22.27 Å
i0_reciprocal	36150000.0000
total_estimate	0.8471
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	21.7 Å
skewness	0.459
kurtosis	-0.397
angular_range	— – 0.3600 Å⁻¹
current_alpha	0.0000
highest_alpha	10090000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.747; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.781; Smooth: 0.985

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	3C-like proteinase nsp5
formula_weight	34314.2 kDa
ec_number	3.4.22.69
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2538

MHHHHHHSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVANPSTPAYTFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVAWLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGTQSVDMLAVKTGVAIEQLLYAIQQLYTGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQ

Source

organism	Middle East respiratory syndrome-related coronavirus
ncbi_taxonomy_id	1335626
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	;N~2~-[(2S,4R)-3-benzyl-4-methyl-2-oxo-1,3,2lambda~5~-oxazaphospholidin-2-yl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide ;
formula_weight	480.5 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	137

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6. Citations (1)

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length_a	102.139 Å
length_b	58.254 Å
length_c	50.187 Å
angle_alpha	90.00 °
angle_beta	112.48 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.900 Å
resolution_low	46.370 Å
r_factor	0.1677
r_work	0.1648
r_free	0.2232

fit	/app/data/saxs_computation/zj/9zjc/9zjc.fit
pddf	/app/data/pr_computation/zj/9zjc/9zjc.pr.out
profile	/app/data/saxs_computation/zj/9zjc/9zjc.dat

Crystal structure of MERS 3CL protease in complex with inhibitor IKR-I-52

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction