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9zj8

Crystal structure of MERS 3CL protease in complex with inhibitor AMJ-II-72

Method: X-RAY DIFFRACTION D_max: 75.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zj8
deposition_date	2025-12-04
last_revision	2026-06-10
title	Crystal structure of MERS 3CL protease in complex with inhibitor AMJ-II-72
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	22.00 Å
rg_electron	21.57 Å
i0	35847400.00
molecular_weight	31046.0 kDa
excluded_volume	30048 Å³
envelope_volume	47778 Å³
shell_volume	19467 Å³
envelope_diameter	76.2 Å
shell_rg	27.07 Å
envelope_rg	21.61 Å
shape_rg	21.59 Å
total_rg	22.07 Å
total_atoms	2333
n_residues	306
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	75.4 Å
rg_real	22.12 Å
rg_real_error	0.51 Å
i0_real	3.5850e+07
i0_real_error	4.4300e+05
rg_reciprocal	22.10 Å
i0_reciprocal	35850000.0000
total_estimate	0.6540
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	21.4 Å
skewness	0.460
kurtosis	-0.394
angular_range	— – 0.3600 Å⁻¹
current_alpha	0.0000
highest_alpha	9643000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.759; Stabil: 1.000; Sysdev: 0.145; Positv: 1.000; Valcen: 0.800; Smooth: 0.985

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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	2388

MHHHHHHSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVANPSTPAYTFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVAWLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGTQSVDMLAVKTGVAIEQLLYAIQQLYTGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQ

Source

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

Entity 2 non-polymer

description	;N~2~-({[(2S,4R)-2-[(4-fluorophenyl)methoxy]-3-(2-methylpropyl)-2-oxo-1,3,2lambda~5~-oxazaphospholidin-4-yl]methoxy}carbonyl)-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide ;
formula_weight	612.6 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	48

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6. Citations (1)

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length_a	100.040 Å
length_b	57.945 Å
length_c	49.478 Å
angle_alpha	90.00 °
angle_beta	112.01 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.100 Å
resolution_low	46.370 Å
r_factor	0.1899
r_work	0.1871
r_free	0.2467

fit	/app/data/saxs_computation/zj/9zj8/9zj8.fit
pddf	/app/data/pr_computation/zj/9zj8/9zj8.pr.out
profile	/app/data/saxs_computation/zj/9zj8/9zj8.dat

Crystal structure of MERS 3CL protease in complex with inhibitor AMJ-II-72

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