PDB-2q3k: Crystal Structure of Lysine Sulfonamide Inhibitor Reveals the Dis...

ID or keywords:

Entry

Database: PDB / ID: 2q3k

Title

Crystal Structure of Lysine Sulfonamide Inhibitor Reveals the Displacement of the Conserved Flap Water Molecule in HIV-1 Protease

Components

Protease

Keywords

VIRAL PROTEIN /

Drug design /

HIV-1 protease /

protease inhibitors

Function / homology

Function and homology information

RNA stem-loop binding /

host cell /

HIV-1 retropepsin /

retroviral ribonuclease H /

exoribonuclease H /

exoribonuclease H activity / host multivesicular body / DNA integration /

RNA-directed DNA polymerase / viral genome integration into host DNA ...
Similarity search - Function

Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain /

Integrase, C-terminal domain superfamily, retroviral /

Integrase, N-terminal zinc-binding domain ...
Similarity search - Domain/homology

Biological species

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Schiffer, C.A. / Nalam, M.N.L.

Citation

Journal: J.Virol. / Year: 2007
Title: Crystal structure of lysine sulfonamide inhibitor reveals the displacement of the conserved flap water molecule in human immunodeficiency virus type 1 protease.
Authors: Nalam, M.N. / Peeters, A. / Jonckers, T.H. / Dierynck, I. / Schiffer, C.A.

History

Deposition	May 30, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 21, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Derived calculations / Version format compliance
Revision 1.2	Oct 18, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3	Oct 20, 2021	Group: Advisory / Database references / Derived calculations Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Aug 30, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2q3k.cif.gz	57.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2q3k.ent.gz	42.4 KB	Display	PDB format
PDBx/mmJSON format	2q3k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q3/2q3k ftp://data.pdbj.org/pub/pdb/validation_reports/q3/2q3k	HTTPS FTP

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Related structure data

Related structure data	1f7aS S: Starting model for refinement
Similar structure data	3oy4-d 3em6-d 3nxn-d 2qi3-d 6pjm-d 4djq-d 1b6l-d 3eky-d 3b7v-d 1t3r-d Search similar-shape structures by Omokage search (details) 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	#6 - Jun 2000 HIV-1 Protease similarity (2) #163 - Jul 2013 HIV Capsid similarity (1)

Deposited unit

A: Protease

B: Protease

hetero molecules

22.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	51.105, 58.097, 61.601
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Protease / Mass: 10815.790 Da / Num. of mol.: 2 / Mutation: Q7K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: SF2 / Gene: pol / Plasmid: PXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP56 / References: UniProt: O38732, UniProt: P03369*PLUS
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-MUW / N-{(5S)-5-[{[4-(AMINOMETHYL)PHENYL]SULFONYL}(ISOBUTYL)AMINO]-6-HYDROXYHEXYL}-NALPHA-(METHOXYCARBONYL)-BETA-PHENYL-L-PHENYLALANINAMIDE Mass: 638.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₄H₄₆N₄O₆S
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.11 Å³/Da / Density % sol: 41.77 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 126 mM sodium phosphate; 63 mM sodium citrate; 24-29% ammonium sulphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 200 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 15, 2005 / Details: osmic mirrors
Radiation	Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. obs: 12879 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / R_merge(I) obs: 0.72 / R_sym value: 0.72 / Net I/σ(I): 13.1

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1F7A

1f7a

Resolution: 2→42.26 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.935 / SU B: 8.829 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2323	619	4.8 %	RANDOM
R_work	0.18676	-	-	-
obs	0.18898	12220	98.82 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 24.819 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.1 Å²	0 Å²	0 Å²
2-	-	-0.32 Å²	0 Å²
3-	-	-	1.42 Å²

Refinement step

Cycle: LAST / Resolution: 2→42.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1490	0	67	110	1667

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	1593
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1534
X-RAY DIFFRACTION	r_angle_refined_deg	1.26	2.025	2169
X-RAY DIFFRACTION	r_angle_other_deg	0.647	3	3552
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.588	5	200
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.808	25	52
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.364	15	260
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.96	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	256
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1727
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	282
X-RAY DIFFRACTION	r_nbd_refined	0.174	0.2	234
X-RAY DIFFRACTION	r_nbd_other	0.188	0.2	1559
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	741
X-RAY DIFFRACTION	r_nbtor_other	0.085	0.2	1025
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.177	0.2	80
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.289	0.2	11
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.205	0.2	61
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.282	0.2	8
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.743	1.5	1059
X-RAY DIFFRACTION	r_mcbond_other	0.196	1.5	416
X-RAY DIFFRACTION	r_mcangle_it	0.96	2	1614
X-RAY DIFFRACTION	r_scbond_it	1.519	3	647
X-RAY DIFFRACTION	r_scangle_it	2.208	4.5	555
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.995→2.047 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.312	36	-
R_work	0.219	844	-
obs	-	-	94.32 %

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	7.2367	-4.4678	-2.5184	5.8335	1.4125	8.2982	-0.0791	0.1776	-0.8795	0.9283	-0.0128	0.6753	0.6836	-0.6229	0.092	0.0088	-0.0134	0.0506	-0.0757	-0.0236	0.0032	20.2533	14.1639	22.326
2	53.3065	-4.6868	-4.6541	9.9464	-0.5984	1.7758	-0.0951	1.6104	-0.6781	-0.1481	0.0634	0.8956	0.0656	-0.5675	0.0316	-0.0742	0.0132	-0.0238	-0.1087	-0.024	0.0117	13.4279	18.2148	16.0872
3	28.5732	3.4678	7.9967	1.652	2.1138	5.4724	0.1614	0.6621	-0.9402	-0.0359	0.0032	0.4095	0.1956	-0.419	-0.1646	-0.069	-0.0085	0.0149	-0.0738	-0.0296	0.0639	6.5613	22.359	16.8042
4	1.6373	-0.5447	4.3844	0.1812	-1.4585	11.7405	-0.1072	-0.3691	0.2231	-0.022	0.1583	0.4399	-0.6264	-0.4651	-0.0511	-0.0854	0.0257	-0.0208	-0.1178	-0.0325	0.0032	12.5642	32.1612	18.0832
5	42.3118	-39.7854	-18.3235	55.6425	3.4888	19.9083	0.2342	1.0275	-0.3756	-0.3264	-0.1747	1.082	1.2727	-1.3739	-0.0595	0.0853	-0.1363	-0.139	0.1024	0.0459	0.0375	1.9732	30.0448	9.2304
6	26.9281	17.4593	-6.3171	22.0339	-8.1137	2.9887	0.3495	-0.4777	2.4648	0.724	0.7035	2.0061	-0.1871	-0.4257	-1.053	-0.0964	0.0558	0.0945	0.0171	0.0757	0.2971	1.4368	39.9831	14.5142
7	83.4841	-52.9502	3.9398	47.2632	3.61	2.914	0.4329	-0.2094	-0.4895	-0.904	0.0805	0.5825	0.2856	0.3092	-0.5134	-0.0395	0.0397	0.0382	-0.0505	0.0033	-0.1297	17.2779	37.7842	11.973
8	6.1367	3.5409	-4.1492	4.5073	-5.3874	6.4415	0.206	-0.2608	0.453	-0.1078	0.1981	0.6654	0.184	-0.0602	-0.404	-0.0609	0.0157	-0.0118	-0.0407	-0.0962	0.059	5.562	32.1079	18.872
9	5.1046	-3.2991	3.9947	5.7971	-5.2492	5.0675	0.2465	0.2892	0.4017	-0.556	-0.2905	0.3795	0.4765	0.1718	0.0439	-0.0934	0.0263	-0.0032	-0.0781	0.0216	-0.004	10.5467	30.2638	15.1896
10	11.8857	-8.853	4.0519	8.869	-1.8852	2.6154	-0.3704	-0.3117	-0.3156	0.5457	0.136	0.3309	0.159	-0.1623	0.2345	-0.0184	0.0476	0.1024	0.0238	0.0264	-0.0866	15.988	24.3215	28.7317
11	9.5293	-1.3452	-2.9545	8.8408	-0.9705	2.6999	-0.2714	-1.0681	0.1374	1.4438	0.3372	-0.2156	0.3511	0.0013	-0.0659	0.1136	0.0609	-0.0149	0.0499	-0.0795	-0.1241	19.8953	27.8418	31.9033
12	34.501	1.6655	0.173	2.5197	0.4825	0.093	0.4725	-0.3054	0.5007	0.2123	-0.3302	-0.0755	-0.4414	-0.0315	-0.1422	-0.056	0.046	0.0027	-0.061	-0.0489	-0.1372	28.134	32.1189	25.7782
13	37.2815	-0.6723	-13.2444	17.453	6.9131	22.7316	-0.2339	0.1492	0.968	-0.2042	0.2664	-1.3109	0.21	0.764	-0.0325	-0.0873	-0.0143	-0.0424	-0.1326	0.032	-0.0436	40.9424	31.6242	22.7181
14	8.5013	3.0081	0.3365	2.9393	-1.8989	2.1853	-0.228	0.1831	0.3941	0.0366	-0.0337	0.3035	-0.0327	0.0482	0.2618	-0.1413	0.0237	0.011	-0.1095	0.0147	-0.1323	25.3141	27.5563	19.8226
15	25.7761	22.75	2.5528	41.7454	-3.639	2.2628	-0.6481	0.3468	0.3601	-0.9276	0.5748	-0.2147	-0.43	-0.2581	0.0732	-0.1111	0.0225	0.0281	-0.0789	0.0263	-0.1936	32.1899	31.0655	13.3676
16	10.579	0.5094	5.5884	6.0951	2.785	10.1633	0.045	0.5476	-0.5923	-0.1093	-0.0038	-0.5972	0.1146	0.7845	-0.0412	-0.0205	0.0157	0.0591	-0.093	0.0453	0.035	36.9994	28.583	5.8803
17	75.7687	-18.9212	-26.6636	4.7251	6.6585	9.3831	-1.2704	1.4611	-0.4476	-0.1493	0.2872	0.9662	0.923	-1.8269	0.9832	0.1998	0.0374	0.1457	0.3634	0.0773	0.2279	23.0944	32.4429	4.5301
18	4.0187	-2.864	0.6512	3.1182	-4.7576	17.2205	0.1899	0.1379	0.0871	-0.0456	-0.3404	-0.2323	0.0821	0.4026	0.1505	-0.1241	-0.053	0.0139	-0.1114	-0.03	-0.0799	38.0651	24.9094	13.8811
19	10.4856	-2.9285	-13.4444	5.0424	11.9689	46.4834	-0.0882	-0.8736	0.2583	0.4818	-0.0638	-0.4751	0.0251	0.6484	0.152	-0.083	-0.0232	-0.0086	-0.104	0.0396	-0.0822	36.7803	20.7098	24.6536
20	1.7974	-0.3008	-0.4493	3.1127	0.2052	1.5086	-0.1373	0.0494	-0.0451	0.1427	0.0985	0.1983	-0.095	-0.1207	0.0388	-0.1148	0.002	-0.0046	-0.0916	0.0285	-0.1282	27.4628	24.2151	18.8215
21	30.0146	-28.996	-27.1396	29.7565	30.0094	48.6484	0.3764	0.6733	0.646	-0.9054	0.2589	-0.8331	-0.4749	-0.2191	-0.6353	-0.0622	0.0033	0.0213	-0.1177	0.0456	-0.0311	20.1342	32.5388	14.6692

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 7	1 - 7
2	X-RAY DIFFRACTION	2	A	A	8 - 12	8 - 12
3	X-RAY DIFFRACTION	3	A	A	13 - 26	13 - 26
4	X-RAY DIFFRACTION	4	A	A	27 - 33	27 - 33
5	X-RAY DIFFRACTION	5	A	A	34 - 37	34 - 37
6	X-RAY DIFFRACTION	6	A	A	38 - 45	38 - 45
7	X-RAY DIFFRACTION	7	A	A	46 - 50	46 - 50
8	X-RAY DIFFRACTION	8	A	A	51 - 74	51 - 74
9	X-RAY DIFFRACTION	9	A	A	75 - 88	75 - 88
10	X-RAY DIFFRACTION	10	A	A	89 - 99	89 - 99
11	X-RAY DIFFRACTION	11	B	B	1 - 7	1 - 7
12	X-RAY DIFFRACTION	12	B	B	8 - 13	8 - 13
13	X-RAY DIFFRACTION	13	B	B	14 - 20	14 - 20
14	X-RAY DIFFRACTION	14	B	B	21 - 29	21 - 29
15	X-RAY DIFFRACTION	15	B	B	30 - 35	30 - 35
16	X-RAY DIFFRACTION	16	B	B	36 - 48	36 - 48
17	X-RAY DIFFRACTION	17	B	B	49 - 55	49 - 55
18	X-RAY DIFFRACTION	18	B	B	56 - 66	56 - 66
19	X-RAY DIFFRACTION	19	B	B	67 - 73	67 - 73
20	X-RAY DIFFRACTION	20	B	B	74 - 99	74 - 99
21	X-RAY DIFFRACTION	21	A	H	200	1

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