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9zjb

Crystal structure of MERS 3CL protease in complex with inhibitor IKR-I-46

Method: X-RAY DIFFRACTION D_max: 76.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zjb
deposition_date	2025-12-04
last_revision	2026-06-10
title	Crystal structure of MERS 3CL protease in complex with inhibitor IKR-I-46
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	22.08 Å
rg_electron	21.61 Å
i0	36054000.00
molecular_weight	31003.0 kDa
excluded_volume	29969 Å³
envelope_volume	48207 Å³
shell_volume	19538 Å³
envelope_diameter	75.9 Å
shell_rg	27.17 Å
envelope_rg	21.72 Å
shape_rg	21.63 Å
total_rg	22.14 Å
total_atoms	2328
n_residues	305
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	76.1 Å
rg_real	22.21 Å
rg_real_error	0.48 Å
i0_real	3.6050e+07
i0_real_error	4.8990e+05
rg_reciprocal	22.19 Å
i0_reciprocal	36050000.0000
total_estimate	0.8435
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	21.6 Å
skewness	0.466
kurtosis	-0.387
angular_range	— – 0.3600 Å⁻¹
current_alpha	0.0000
highest_alpha	9978000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.743; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.782; Smooth: 0.951

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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	2461

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,4S)-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	94

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6. Citations (1)

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length_a	101.677 Å
length_b	57.830 Å
length_c	49.760 Å
angle_alpha	90.00 °
angle_beta	112.08 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.880 Å
resolution_low	41.710 Å
r_factor	0.1693
r_work	0.1668
r_free	0.2156

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

Crystal structure of MERS 3CL protease in complex with inhibitor IKR-I-46

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