PDB-4dqh: Crystal Structure of (R14C/E65C) HIV-1 Protease in complex with DRV

ID or keywords:

Entry

Database: PDB / ID: 4dqh

Title

Crystal Structure of (R14C/E65C) HIV-1 Protease in complex with DRV

Components

Wild-type HIV-1 protease dimer

Keywords

HYDROLASE/HYDROLASE INHIBITOR /

HIV-1 protease /

drug resistance /

drug design /

Protease inhibitors /

AIDS / HYDROLASE-HYDROLASE INHIBITOR complex

Function / homology

Function and homology information

: / : /

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 /

SYNCHROTRON / Resolution: 1.79 Å

Authors

Schiffer, C.A. / Mittal, S.

Citation

Journal: J.Am.Chem.Soc. / Year: 2012
Title: Hydrophobic core flexibility modulates enzyme activity in HIV-1 protease.
Authors: Mittal, S. / Cai, Y. / Nalam, M.N. / Bolon, D.N. / Schiffer, C.A.

History

Deposition	Feb 15, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 7, 2012	Provider: repository / Type: Initial release
Revision 1.1	May 2, 2012	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dq/4dqh ftp://data.pdbj.org/pub/pdb/validation_reports/dq/4dqh	HTTPS FTP

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Related structure data

Related structure data	4dqbC 4dqcC 4dqeC 4dqfC 4dqgC C: citing same article (ref.)
Similar structure data	6pje-d 1t7j-d 6oy1-d 1bv9-d 3mxd-d 3saa-d 1mer-d 3em3-d 3o9i-d 4gb2-d 3mxe-d 1mrw-d 1t7i-d 6oy2-d 1n49-2 1d4j-d 3o99-d 1k6c-d 6oxp-d 2qi1-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: Wild-type HIV-1 protease dimer

B: Wild-type HIV-1 protease dimer

hetero molecules

22 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)	50.706, 57.982, 61.546
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Wild-type HIV-1 protease dimer Mass: 10687.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: SF2 / Gene: gag-pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP56 / References: UniProt: P12499*PLUS
#2: Chemical	ChemComp-017 / (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE / Darunavir / TMC114 / UIC-94017 / Darunavir Mass: 547.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₇H₃₇N₃O₇S / Comment: medication, antiretroviral*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.12 Å³/Da / Density % sol: 41.88 %
Crystal grow	Method: vapor diffusion, hanging drop / pH: 5 Details: 50mM Citrate phosphate buffer pH 5.0, 7% DMSO, 24-35% Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 14-BM-C / Wavelength: 0.9 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2009

Radiation

Monochromator: Bent Ge(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9 Å / Relative weight: 1

Reflection

Resolution: 1.79→50 Å / Num. obs: 17513 / % possible obs: 99 % / Redundancy: 6.9 % / R_merge(I) obs: 0.071 / Net I/σ(I): 10.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.79-1.85	6.1	0.417	1	97.1
1.85-1.93	6.9	0.293	1	97.5
1.93-2.02	6.9	0.211	1	98.4
2.02-2.12	6.9	0.161	1	99.1
2.12-2.26	7	0.133	1	98.9
2.26-2.43	7	0.116	1	99.4
2.43-2.67	7	0.092	1	99.7
2.67-3.06	7.1	0.069	1	99.9
3.06-3.86	7	0.048	1	100
3.86-50	6.7	0.036	1	99.4

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction

Refinement

Resolution: 1.79→42.22 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.941 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 4.659 / SU ML: 0.079 / SU R Cruickshank DPI: 0.1366 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21879	889	5.1 %	RANDOM
R_work	0.17028	-	-	-
obs	0.17262	16582	98.64 %	-

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: 19.942 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.32 Å²	0 Å²	0 Å²
2-	-	0.37 Å²	0 Å²
3-	-	-	0.95 Å²

Refinement step

Cycle: LAST / Resolution: 1.79→42.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1468	0	44	138	1650

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	1600
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1057
X-RAY DIFFRACTION	r_angle_refined_deg	1.367	2.004	2192
X-RAY DIFFRACTION	r_angle_other_deg	0.797	3	2614
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.816	5	210
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.487	25.094	53
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.722	15	259
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.797	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	267
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	1772
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	298
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.789→1.835 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.295	57	-
R_work	0.212	1026	-
obs	-	-	91.62 %

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	1.5333	-1.455	-0.8363	1.4572	0.1987	5.8888	-0.0832	0.0283	-0.2019	0.0919	-0.0345	0.1626	0.0591	0.0239	0.1177	0.0727	-0.0145	-0.0015	0.0129	0.0087	0.1032	19.7731	13.9692	23.7032
2	9.584	0.7805	-2.205	0.2202	0.19	1.3798	0.0513	0.248	0.0925	-0.0057	0.0465	-0.0184	-0.0408	0.0296	-0.0978	0.0232	-0.0016	0.0053	0.0274	0.0147	0.0678	14.5984	18.5868	16.6219
3	4.3471	-0.876	1.0401	2.2256	1.0861	1.0683	-0.1249	0.1005	0.144	-0.0153	0.0386	0.0568	-0.0531	0.065	0.0863	0.0133	-0.0001	0.0069	0.0194	0.0176	0.0332	-0.1348	24.4475	17.7194
4	4.9159	1.1883	2.123	1.2582	1.3651	1.6856	0.0086	0.104	-0.02	-0.0245	-0.009	-0.0557	-0.0301	0.0055	0.0004	0.025	0.0049	-0.0082	0.02	0.0061	0.0862	7.7994	21.6569	16.4417
5	2.5005	0.7633	0.532	2.3482	0.3809	0.266	-0.0149	0.0953	0.0749	0.04	-0.0716	0.1057	-0.0384	0.1234	0.0865	0.0561	-0.028	-0.0117	0.1148	0.0383	0.067	16.9051	31.0052	21.6656
6	1.7336	0.7758	1.7368	0.3522	0.679	4.1836	0.0107	0.0744	-0.0463	0.0065	0.0461	-0.0241	0.0514	-0.0754	-0.0568	0.0429	0.0075	-0.0154	0.0387	0.0053	0.0585	5.6934	30.5157	13.1225
7	2.9111	1.4179	0.4118	10.5695	1.3823	0.2001	-0.0934	0.0012	-0.002	0.0519	0.0553	0.3776	-0.0009	0.0016	0.0381	0.0309	-0.0184	0.0249	0.0784	0.0309	0.0598	-2.5587	37.1964	14.8813
8	11.1339	-2.4432	-4.1423	2.1342	1.6731	1.9065	-0.0661	0.0258	0.2943	0.2239	0.142	-0.0059	0.1268	0.0585	-0.0759	0.0562	0.0037	0.0188	0.0555	0.0045	0.0444	8.0162	43.935	15.4212
9	7.027	-4.0659	-1.5575	2.4131	0.8903	0.3479	0.0363	0.0419	0.1068	-0.0134	-0.0104	-0.0119	-0.0016	-0.0127	-0.0259	0.062	0.0058	0.0132	0.0387	0.0035	0.0446	15.9144	38.5249	10.4845
10	2.4916	1.8487	-2.9255	2.5507	-3.1859	5.5868	-0.0247	0.0396	-0.1034	0.0585	-0.0003	0.0199	-0.2083	-0.0803	0.025	0.0474	0.0163	0.0183	0.0301	0.0007	0.0676	2.8144	38.4916	17.0568
11	1.6032	-3.4823	0.5886	13.9813	-2.8273	0.5905	0.0711	0.0467	-0.0081	0.0327	-0.0179	0.2556	-0.0133	0.0031	-0.0532	0.068	0.0149	-0.0008	0.067	0.009	0.0439	1.7568	28.922	24.5157
12	0.3307	-0.7738	-0.7916	5.2588	-0.3341	3.307	-0.0772	0.0067	-0.0745	0.4248	-0.0074	0.3294	0.0518	0.018	0.0845	0.0487	0.0086	0.0103	0.0583	0.0139	0.0667	3.6392	25.6585	27.6407
13	0.0815	-0.1784	0.2674	0.9757	0.7134	3.7636	0.0132	0.002	0.0098	-0.0358	0.0166	-0.0474	-0.0263	0.0381	-0.0298	0.0407	0.0087	-0.0107	0.0517	0.0051	0.0711	7.7285	34.0583	12.9664
14	0.5837	-1.0109	1.5381	4.6028	-2.4628	4.9495	0.0272	0.0788	-0.042	-0.2563	-0.2024	0.0665	0.1061	0.278	0.1752	0.0656	0.0222	0.0016	0.0368	0.0121	0.1004	11.9578	27.0264	14.2043
15	3.0448	-1.2057	-1.6176	2.6303	-0.4701	1.4326	0.0259	-0.1372	0.0028	-0.0567	-0.0097	0.019	0.0069	0.0996	-0.0162	0.0488	0.011	0.0033	0.0643	0.0066	0.0347	13.1774	30.1981	26.5529
16	13.5518	-5.7049	0.181	3.31	0.1653	0.4011	-0.356	-0.4309	-0.0487	0.2077	0.306	0.0752	0.0562	0.0539	0.05	0.047	0.0298	0.0176	0.0658	0.0138	0.0096	18.2404	22.909	30.3741
17	1.9846	-2.3154	0.9998	5.23	-1.0814	3.0033	-0.0955	-0.2183	0.1407	0.1999	0.0635	-0.1912	-0.112	-0.0412	0.032	0.0564	0.0086	0.0036	0.074	-0.0141	0.0157	20.892	26.5776	33.2393
18	11.891	-0.2567	-1.3814	0.1284	0.082	0.1827	-0.1002	-0.3464	0.5269	-0.0767	0.1271	0.0415	-0.0214	0.0855	-0.0269	0.0952	-0.038	-0.0341	0.1279	0.0236	0.0677	25.7274	32.8034	26.9028
19	7.1932	-3.0854	-5.9953	1.3327	2.5789	5.0039	-0.008	-0.2226	0.3734	0.0443	0.2179	-0.1471	0.0854	0.211	-0.2099	0.0172	0.006	0.0194	0.1678	0.0233	0.0617	40.5117	30.3056	21.1599
20	7.177	3.1383	0.6042	1.4417	0.4632	0.8715	-0.0239	0.0371	0.0621	-0.0275	0.0232	0.0366	-0.0172	-0.0949	0.0006	0.0424	-0.003	-0.0008	0.0547	0.0039	0.03	32.4485	32.4431	23.2626
21	1.9613	-0.056	0.3008	0.1653	0.0041	0.048	0.0213	0.0938	0.0398	0.024	0.0007	-0.0418	0.0124	0.0147	-0.022	0.0618	0.0001	-0.0097	0.0515	0.0018	0.063	23.2822	24.266	16.2338
22	5.3909	4.907	-0.6616	12.2459	-1.0561	0.1241	0.1123	0.0513	0.1932	-0.0695	-0.1482	0.0066	-0.0084	0.02	0.0359	0.053	0.0028	-0.0024	0.078	0.0161	0.09	32.8238	32.6031	13.6324
23	4.4574	0.816	1.4248	0.3613	1.1208	3.9879	0.2649	-0.1542	-0.0996	0.015	0.0403	-0.0924	-0.013	0.2183	-0.3053	0.0662	-0.0161	-0.0063	0.0774	0.0151	0.0953	43.1226	30.6574	11.417
24	15.064	-3.5485	0.5032	1.2672	-0.607	0.6421	0.149	0.4365	-0.1842	0.059	-0.1713	0.0602	-0.1208	0.1683	0.0223	0.064	-0.0075	-0.0016	0.1097	0.0173	0.0562	33.7665	27.8379	2.7811
25	7.6541	-1.2497	-4.1758	0.5434	-0.0026	3.9829	-0.0156	0.0321	0.0359	-0.034	0.0162	-0.0431	0.1538	-0.0645	-0.0006	0.0554	0.0165	-0.0049	0.0238	-0.003	0.0194	21.1223	31.8697	5.9724
26	5.1785	-3.7973	2.0045	6.2563	-4.1707	3.1322	0.0886	0.1364	-0.0463	-0.0761	-0.1391	-0.1444	0.0019	0.181	0.0504	0.0434	0.0111	0.014	0.0738	-0.0096	0.0431	36.0298	28.7062	6.6139
27	0.4787	-1.0065	0.7312	2.9129	0.7131	7.546	-0.0128	0.0862	-0.0237	0.0679	-0.1709	0.1347	-0.0115	0.0891	0.1837	0.0545	0.011	0.0138	0.0604	0.0015	0.096	39.7602	21.4673	15.0916
28	7.6599	-0.6774	-5.1337	4.5449	2.1505	6.1812	0.0874	-0.262	0.1906	0.2061	0.1	-0.0346	-0.021	0.317	-0.1874	0.061	0.0177	-0.0117	0.0337	-0.0037	0.065	35.8282	22.9722	26.9653
29	0.7359	-0.6407	0.5629	1.9619	-0.8123	0.9077	-0.0219	0.1127	-0.0277	-0.1199	-0.0208	-0.069	0.0285	0.0494	0.0427	0.0438	-0.003	0.0139	0.0402	0.0011	0.0408	33.7836	27.1824	12.6457
30	1.2619	1.1291	-0.3275	1.0201	-0.1778	2.1806	0.0139	0.0599	0.0833	-0.005	0.0533	0.0817	-0.0643	-0.1145	-0.0673	0.0501	0.0042	-0.0037	0.0379	0.0147	0.0587	27.7227	31.5537	17.4349
31	1.6056	-0.2801	-0.1067	0.8581	-0.6475	1.2759	-0.0696	-0.0613	-0.0276	0.027	0.0425	0.0173	-0.0116	0.0338	0.0271	0.05	0.0002	0.0027	0.0352	0.0067	0.0496	28.5599	18.7749	20.0506
32	6.4555	-0.4487	-1.3236	3.0795	0.8275	0.4524	-0.3377	-0.0651	-0.2837	0.1978	0.2153	0.1842	0.1209	0.0545	0.1224	0.0631	0.0152	0.0517	0.051	0.0041	0.0675	17.8194	18.2106	28.1189

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 6
2	X-RAY DIFFRACTION	2	A	7 - 12
3	X-RAY DIFFRACTION	3	A	13 - 18
4	X-RAY DIFFRACTION	4	A	19 - 24
5	X-RAY DIFFRACTION	5	A	25 - 30
6	X-RAY DIFFRACTION	6	A	31 - 36
7	X-RAY DIFFRACTION	7	A	37 - 42
8	X-RAY DIFFRACTION	8	A	43 - 46
9	X-RAY DIFFRACTION	9	A	47 - 56
10	X-RAY DIFFRACTION	10	A	57 - 60
11	X-RAY DIFFRACTION	11	A	61 - 66
12	X-RAY DIFFRACTION	12	A	67 - 74
13	X-RAY DIFFRACTION	13	A	75 - 80
14	X-RAY DIFFRACTION	14	A	81 - 85
15	X-RAY DIFFRACTION	15	A	86 - 91
16	X-RAY DIFFRACTION	16	A	92 - 99
17	X-RAY DIFFRACTION	17	B	1 - 6
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