PDB-9lgp: Crystal structure of the HRV B14 3C protease in complex with AG7404

ID or keywords:

Entry

Database: PDB / ID: 9lgp

Title

Crystal structure of the HRV B14 3C protease in complex with AG7404

Components

Genome polyprotein

Keywords

HYDROLASE / 3C protease / HRV / complex / AG7404 / Rhinoviruse

Function / homology

Function and homology information

lysis of host organelle involved in viral entry into host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity ...
Similarity search - Function

Biological species

rhinovirus B14

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.11 Å

Authors

Lee, J. / Kim, H. / Jo, I.

Funding support

Korea, Republic Of, 2items

Citation

Journal: Iucrj / Year: 2026
Title: Structural insights into the antiviral efficacy of AG7404 against human rhinovirus 3C proteases.
Authors: Lee, J. / Lee, H.L. / Kim, H. / Gil, Y. / Lee, S.H. / Jung, Y.S. / Shin, J.S. / Jo, I.

History

Deposition	Jan 10, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9lgp.cif.gz	290.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9lgp.ent.gz	236.9 KB	Display	PDB format
PDBx/mmJSON format	9lgp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9lgp_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	9lgp_full_validation.pdf.gz	1.5 MB	Display
Data in XML	9lgp_validation.xml.gz	41.5 KB	Display
Data in CIF	9lgp_validation.cif.gz	54.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lg/9lgp ftp://data.pdbj.org/pub/pdb/validation_reports/lg/9lgp	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#20 - Aug 2001 Poliovirus and Rhinovirus similarity (23) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

Deposited unit

A: Genome polyprotein

B: Genome polyprotein

C: Genome polyprotein

D: Genome polyprotein

hetero molecules

82.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Genome polyprotein

hetero molecules

defined by author
20.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Genome polyprotein

hetero molecules

defined by author
20.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Genome polyprotein

hetero molecules

defined by author
20.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Genome polyprotein

hetero molecules

defined by author
20.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	32.880, 148.660, 67.410
Angle α, β, γ (deg.)	90.00, 92.62, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Genome polyprotein Mass: 20021.877 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) rhinovirus B14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03303
#2: Chemical	ChemComp-XNV / ethyl (4R)-4-({(2S)-2-[3-{[(5-methyl-1,2-oxazol-3-yl)carbonyl]amino}-2-oxopyridin-1(2H)-yl]pent-4-ynoyl}amino)-5-[(3S)-2-oxopyrrolidin-3-yl]pentanoate / AG7404, bound form Mass: 525.554 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₆H₃₁N₅O₇ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 691 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.05 Å³/Da / Density % sol: 40.14 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Tris-HCl, 0.8 M Lithium chloride, 36%(w/v) PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00003 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 12, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00003 Å / Relative weight: 1
Reflection	Resolution: 2.11→29.47 Å / Num. obs: 36418 / % possible obs: 98.22 % / Redundancy: 7 % / CC_1/2: 0.993 / CC star: 0.998 / R_merge(I) obs: 0.154 / R_pim(I) all: 0.062 / R_rim(I) all: 0.166 / Net I/σ(I): 11.6
Reflection shell	Resolution: 2.11→2.185 Å / R_merge(I) obs: 0.6351 / Mean I/σ(I) obs: 4.46 / Num. unique obs: 3622 / CC_1/2: 0.883 / CC star: 0.968 / R_pim(I) all: 0.2546 / R_rim(I) all: 0.685 / % possible all: 96.77

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data scaling
PHASER		phasing
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.11→29.47 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.73 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2672	1820	5 %
R_work	0.2249	-	-
obs	0.227	36414	98.21 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.11→29.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5480	0	152	691	6323

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.001
X-RAY DIFFRACTION	f_angle_d	0.68
X-RAY DIFFRACTION	f_dihedral_angle_d	11.419	820
X-RAY DIFFRACTION	f_chiral_restr	0.043	898
X-RAY DIFFRACTION	f_plane_restr	0.003	998

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.11-2.17	0.3927	138	0.3005	2620	X-RAY DIFFRACTION	97
2.17-2.23	0.2973	138	0.2688	2638	X-RAY DIFFRACTION	98
2.23-2.3	0.3119	140	0.261	2655	X-RAY DIFFRACTION	98
2.3-2.38	0.3125	140	0.2628	2652	X-RAY DIFFRACTION	98
2.39-2.48	0.2894	138	0.2517	2628	X-RAY DIFFRACTION	98
2.48-2.59	0.2921	141	0.2481	2676	X-RAY DIFFRACTION	99
2.59-2.73	0.2702	141	0.2375	2684	X-RAY DIFFRACTION	98
2.73-2.9	0.3128	139	0.2425	2633	X-RAY DIFFRACTION	99
2.9-3.12	0.2853	140	0.2258	2670	X-RAY DIFFRACTION	99
3.12-3.44	0.254	142	0.2081	2693	X-RAY DIFFRACTION	99
3.44-3.93	0.2074	141	0.185	2687	X-RAY DIFFRACTION	99
3.94-4.95	0.2118	142	0.1737	2694	X-RAY DIFFRACTION	99
4.95-29.47	0.2199	140	0.2077	2664	X-RAY DIFFRACTION	97

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.3961	0.4075	-0.0124	0.7362	-0.3022	1.9303	-0.0415	-0.092	-0.0743	0.0125	-0.061	0.0831	0.0674	-0.2242	0.0422	0.0862	-0.0193	-0.0346	0.0459	0.0108	0.1106	12.4628	-6.4526	26.3517
2	1.5469	-0.004	-0.0066	1.0896	0.2681	0.2597	-0.0619	-0.0669	0.0374	0.133	0.0479	0.1014	-0.0495	0.0106	-0.0164	0.0189	-0.0124	0.0349	0.0946	0.0391	0.0913	4.9565	-2.1204	24.1037
3	1.0043	-0.1961	0.5527	0.6858	-0.0343	1.2161	-0.0049	-0.0545	0.0668	-0.0006	0.0292	0.117	-0.079	0.0066	-0.0041	0.0441	-0.0033	-0.0002	0.0484	0.0164	0.0934	17.4859	6.2048	22.823
4	1.246	-0.5537	-0.5096	0.2619	0.1431	0.6212	-0.0004	0.22	-0.3331	-0.0632	-0.0564	0.0391	0.0319	-0.177	0.7316	0.0763	0.0655	-0.0154	0.131	-0.0867	0.1441	13.3392	1.113	16.9828
5	2.2033	-0.4294	0.0672	2.871	0.5556	1.3458	-0.064	0.0309	-0.1109	-0.2095	0.0366	-0.0335	0.0321	0.0724	0.0343	0.0735	0.0197	-0.0083	0.0767	-0	0.0739	-0.0266	-8.3536	50.4915
6	1.4725	0.2124	0.6857	1.6195	-0.6302	0.6543	0.1294	-0.0997	-0.0432	-0.0019	0.019	-0.2088	0.1046	-0.1074	-0.0413	0.0678	-0.0284	0.0105	0.1551	-0.0446	0.1184	2.6113	-9.2248	58.9068
7	1.5355	-1.2001	0.0812	1.5067	-0.3724	0.1728	-0.0448	-0.2314	0.2571	0.1923	0.017	-0.1855	0.0643	-0.1847	-0.0476	0.0625	-0.008	0.0122	0.1894	0.0175	0.0683	0.5912	4.8839	53.4502
8	0.4202	0.4411	-0.3279	0.5263	-0.1589	0.8277	0.0315	-0.1278	0.1932	-0.0431	0.0629	0.1051	-0.0692	0.0326	-0.0629	0.0949	0.0279	0.0408	0.0864	-0.0486	0.1546	-5.3248	4.0544	59.4684
9	1.3774	0.3258	-0.2648	1.0053	0.0577	0.8949	-0.0528	-0.1718	-0.079	0.2409	0.0393	0.0082	-0.0866	0.0323	-0.0013	0.0672	0.0018	0.0409	0.0803	-0.0218	0.0665	19.8618	39.4271	51.5243
10	0.8646	0.0093	-0.1688	0.1344	-0.1277	2.477	0.049	0.1828	0.2538	-0.0231	0.0675	-0.0542	-0.1879	0.0617	0.1923	0.0208	0.0234	-0.0257	0.0952	0.0241	0.1535	17.8755	46.0393	40.2027
11	0.9571	-0.1025	-0.0611	0.1515	-0.2095	0.3322	0.019	-0.0228	-0.016	0.0346	-0.1738	0.1828	0.0653	-0.0725	-0.1183	0.0857	0.0492	0.0248	0.1119	-0.0936	0.1111	26.9205	37.1231	45.7643
12	1.4732	-0.2129	0.2208	0.9378	-0.3457	1.2112	0.0767	-0.0675	-0.1723	0.0145	0.007	0.0778	0.156	-0.1008	-0.032	0.0423	-0.0033	-0.0125	0.0529	-0.0271	0.097	14.8955	29.7005	43.5382
13	1.2334	0.731	0.5861	1.2297	0.2489	0.8366	0.0572	0.0671	-0.3397	-0.012	0.0425	-0.059	0.2664	-0.1698	-0.1086	0.1872	-0.1352	0.039	0.2312	-0.0797	0.1731	-11.4811	24.8562	1.9424
14	1.1039	-0.1568	-0.0643	0.7068	-0.3805	0.4163	0.0011	0.1129	0.3268	0.1188	0.1341	0.1382	-0.1237	-0.0637	-0.0607	0.0312	0.0032	-0.0037	0.0672	0.0261	0.1657	-2.9111	42.6625	5.0616
15	1.048	0.1435	0.3143	0.217	-0.0385	0.2439	-0.0254	0.0155	0.3245	-0.0069	-0.02	0.0848	-0.0759	-0.0415	-0.0873	0.0135	0.0179	0.0226	0.0412	0.0413	0.1477	-7.1223	41.1281	12.582
16	0.9037	0.1762	0.2001	0.6846	-0.3604	0.4822	-0.0458	0.0576	-0.1554	-0.1024	-0.066	-0.1757	0.014	0.0657	0.0121	0.0594	-0.008	0.0494	0.0379	-0.0175	0.0868	-3.6481	24.8787	10.5855
17	1.4104	-0.1811	-0.4192	0.4691	-0.0138	0.3906	-0.0054	-0.1378	-0.0729	0.1132	-0.0373	-0.1176	0.052	0.026	-0.0371	0.0185	-0.0177	-0.003	0.0032	0.0319	0.1248	0.8306	29.5801	15.6626

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 71 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 72 through 97 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 98 through 163 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 164 through 180 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 61 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 62 through 86 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 87 through 110 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 111 through 178 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 2 through 51 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 52 through 71 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 72 through 97 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 98 through 179 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 3 through 13 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 14 through 61 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 62 through 86 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 87 through 122 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 123 through 179 )

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