PDB-4q1y: Mutations Outside the Active Site of HIV-1 Protease Alter Enzyme ...

ID or keywords:

Entry

Database: PDB / ID: 4q1y

Title

Mutations Outside the Active Site of HIV-1 Protease Alter Enzyme Structure and Dynamic Ensemble of the Active Site to Confer Drug Resistance

Components

aspartyl protease

Keywords

hydrolase/hydrolase inhibitor / HIV-1 protease / AIDS / inhibitor complex / hydrolase-hydrolase inhibitor complex

Function / homology

Function and homology information

integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...
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 ...
Similarity search - Domain/homology

Biological species

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Ragland, D.A. / Nalam, M.N.L. / Cao, H. / Nalivaika, E.A. / Cai, Y. / Kurt-Yilmaz, N. / Schiffer, C.A.

Citation

Journal: J.Am.Chem.Soc. / Year: 2014
Title: Drug resistance conferred by mutations outside the active site through alterations in the dynamic and structural ensemble of HIV-1 protease.
Authors: Ragland, D.A. / Nalivaika, E.A. / Nalam, M.N. / Prachanronarong, K.L. / Cao, H. / Bandaranayake, R.M. / Cai, Y. / Kurt-Yilmaz, N. / Schiffer, C.A.

History

Deposition	Apr 4, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 18, 2015	Provider: repository / Type: Initial release
Revision 1.1	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_ref_seq_dif / 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_ref_seq_dif.details / _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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Download

PDBx/mmCIF format	4q1y.cif.gz	96.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4q1y.ent.gz	76.2 KB	Display	PDB format
PDBx/mmJSON format	4q1y.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4q1y_validation.pdf.gz	822.7 KB	Display	wwPDB validaton report
Full document	4q1y_full_validation.pdf.gz	826.8 KB	Display
Data in XML	4q1y_validation.xml.gz	12 KB	Display
Data in CIF	4q1y_validation.cif.gz	16.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q1/4q1y ftp://data.pdbj.org/pub/pdb/validation_reports/q1/4q1y	HTTPS FTP

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Related structure data

Related structure data	4q1wC 4q1xC C: citing same article (ref.)
Similar structure data	4eq0-d 2psv-d 2nxl-d 1t3r-d 2qhy-d 7hvp-d 4njt-1 4djq-d 3o9d-d 3i7e-d 6pu8-d 4rvx-1 3bgc-d 4hvp-d 6oxz-d 2qi6-d 1mer-d 1d4k-d 2fxd-d 2qi0-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 (13) #163 - Jul 2013 HIV Capsid similarity (13) #33 - Sep 2002 HIV Reverse Transcriptase similarity (12) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #169 - Jan 2014 HIV Envelope Glycoprotein similarity (1) #63 - Mar 2005 T-Cell Receptor similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#6 - Jun 2000
HIV-1 Protease
similarity (13)
#163 - Jul 2013
HIV Capsid
similarity (13)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (12)
#205 - Jan 2017
Nuclear Pore Complex
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#169 - Jan 2014
HIV Envelope Glycoprotein
similarity (1)
#63 - Mar 2005
T-Cell Receptor
similarity (1)

Deposited unit

A: aspartyl protease

B: aspartyl protease

hetero molecules

22.7 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)	50.813, 58.225, 61.824
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	aspartyl protease / Pol protein Mass: 10863.833 Da / Num. of mol.: 2 / Fragment: unp residues 1-99 / Mutation: Q7K, V32I, L33F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: HIV-1 M:B_HXB2R / Gene: gag-pol, pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): Tap56 References: UniProt: V5Y949, UniProt: P04585*PLUS, HIV-1 retropepsin
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: 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 Mass: 547.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₇H₃₇N₃O₇S / Comment: medication, antiretroviral*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.1 Å³/Da / Density % sol: 41.56 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 126mM Phosphate buffer, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2008 / Details: Bent conical Si-mirror (Rh coated)
Radiation	Monochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9002 Å / Relative weight: 1
Reflection	Resolution: 1.5→39.25 Å / Num. all: 29633 / Num. obs: 29633 / % possible obs: 98.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.5 % / R_merge(I) obs: 0.048 / Net I/σ(I): 16.8
Reflection shell	Resolution: 1.5→1.55 Å / Redundancy: 5 % / % possible all: 96.7

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Processing

Software

Name	Version	Classification
REFMAC	5.3.0037	refinement
ADSC	Quantum	data collection
HKL-3000		data reduction
HKL-3000		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→39.25 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.946 / SU B: 2.353 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20737	1497	5.1 %	RANDOM
R_work	0.18253	-	-	-
obs	0.1838	28079	98.72 %	-
all	-	29773	-	-

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: 25.341 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.22 Å²	0 Å²	0 Å²
2-	-	1.26 Å²	0 Å²
3-	-	-	-0.04 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→39.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1506	0	65	124	1695

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	1680
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1130
X-RAY DIFFRACTION	r_angle_refined_deg	1.497	2.019	2296
X-RAY DIFFRACTION	r_angle_other_deg	0.876	3	2789
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.237	5	214
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.325	24.915	59
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.65	15	284
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.289	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	265
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1852
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	311
X-RAY DIFFRACTION	r_nbd_refined	0.199	0.2	258
X-RAY DIFFRACTION	r_nbd_other	0.204	0.2	1189
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	781
X-RAY DIFFRACTION	r_nbtor_other	0.088	0.2	946
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.144	0.2	65
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	0.095	0.2	11
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.131	0.2	40
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.185	0.2	16
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	0.817	1.5	1106
X-RAY DIFFRACTION	r_mcbond_other	0.199	1.5	430
X-RAY DIFFRACTION	r_mcangle_it	1.116	2	1694
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.768	3	694
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.464	4.5	602
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.501→1.54 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.207	97	-
R_work	0.207	1963	-
obs	-	-	94.11 %

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	3.8901	-0.6172	-1.3341	2.6186	0.1928	2.2982	-0.1319	-0.4472	0.0343	0.4633	0.1155	-0.0348	-0.0878	0.0761	0.0164	0.011	0.0475	0.0018	-0.0102	-0.0015	-0.1076	20.8698	25.8682	29.414
2	3.7104	-2.6582	-0.2634	3.341	0.3102	3.6035	-0.1935	-0.0906	-0.4888	0.2457	0.0877	0.2781	0.269	-0.1084	0.1058	-0.0125	-0.0034	0.048	-0.0802	0.0213	-0.0195	19.568	17.6066	23.1407
3	3.4443	0.6262	0.206	3.1173	-0.0315	1.0774	-0.0593	0.0102	0.016	-0.0004	-0.0215	-0.1617	-0.08	0.0591	0.0808	-0.0209	0.0059	-0.0058	-0.0525	0.0049	-0.0449	27.9147	28.4849	18.7528
4	4.1698	-1.2131	-1.0038	2.4759	-0.6501	3.2368	0.0072	0.1894	-0.2624	-0.149	0.0348	0.1757	-0.0881	-0.2708	-0.042	-0.0219	0.0243	0.0041	-0.0462	0.0047	-0.0268	12.3745	26.9936	18.4056
5	10.4677	-7.2497	0.9067	7.5405	0.4737	6.9406	-0.1245	-0.0996	0.4454	0.0928	-0.1849	-0.9546	-0.0272	0.3907	0.3094	-0.0571	-0.0255	-0.0546	-0.0548	0.0599	0.1014	39.5385	30.4311	24.0953
6	27.1103	-7.229	-1.7038	8.1131	2.9923	6.5864	0.1833	0.2923	-1.282	-0.4361	-0.0774	0.6189	0.0159	-1.1562	-0.1058	-0.0777	-0.0417	0.0216	0.1345	-0.0151	0.0389	0.8677	21.5718	18.0701
7	3.4069	0.5541	0.1042	6.0197	5.882	8.5068	0.1104	0.1468	0.18	0.0882	0.3222	-1.0335	-0.1235	0.9279	-0.4326	-0.0399	0.0083	-0.0101	0.0583	0.0295	0.1152	39.537	31.5479	10.8237
8	4.3036	-2.953	1.095	20.579	1.9458	2.6766	-0.3466	0.1766	-0.258	0.0356	0.8375	1.3855	0.0599	-0.8309	-0.4909	-0.0116	0.037	0.0464	0.2585	0.2043	0.0575	1.0344	34.2572	13.6866
9	10.3693	-0.8869	-1.0664	0.8247	-0.0478	2.8535	-0.0094	0.2895	0.0083	-0.1791	-0.003	-0.0398	0.053	0.0517	0.0123	-0.0111	0.0167	0.0227	-0.0393	0.0022	-0.0594	28.1118	30.5377	4.1673
10	12.3893	-5.6499	-1.7232	4.5015	-1.5992	4.3188	-0.039	-0.0737	0.1685	0.1569	0.204	0.0287	-0.1859	-0.2413	-0.165	-0.0206	0.0098	0.0065	-0.0503	0.0037	-0.0441	12.6441	39.6951	11.4204
11	1.6877	-0.0779	-1.9186	3.3155	-1.1035	4.1029	0.021	0.145	0.0686	0.088	0.0433	0.0961	-0.1706	-0.0015	-0.0643	-0.0102	-0.0139	-0.0205	-0.059	0.0129	-0.0188	29.2466	33.4103	14.4311
12	2.9058	-3.058	4.0976	5.4062	-4.1959	6.2254	0.1951	0.4007	-0.1361	-0.3012	-0.0382	0.2694	0.3859	0.2143	-0.1569	-0.0403	0.0313	-0.0123	0.0396	0.0027	-0.0592	10.5562	29.4901	12.0432
13	2.515	-1.8895	-0.62	3.8693	-1.0877	3.2601	-0.0603	-0.0389	-0.1604	0.0682	-0.0703	-0.1908	-0.0006	0.0478	0.1306	-0.0284	0.0084	0.0031	-0.0713	0.0122	0.0054	28.6067	19.3982	19.3915
14	6.7473	-2.5083	-3.0346	4.0498	-0.5406	3.8383	-0.1978	-0.3304	-0.1186	0.2053	0.2182	0.1361	-0.1497	-0.1243	-0.0204	-0.0057	0.0579	0.0363	0.0003	0.0198	-0.0659	11.858	29.1458	27.0784
15	6.7272	-0.9619	4.9135	7.9557	-11.8961	21.3885	0.1106	0.2178	-0.5709	-0.5125	-0.307	-0.204	0.6967	0.7034	0.1963	-0.0662	0.0673	0.0791	-0.0417	0.0098	0.0502	38.921	23.1655	10.4267
16	11.1631	11.6664	-12.3379	16.797	-16.5483	20.5429	0.4743	0.0324	0.601	0.8826	0.2704	0.6636	-0.8251	-0.4495	-0.7448	-0.0545	0.1833	0.0869	0.0419	0.1069	0.0083	1.8411	36.8823	21.1092
17	24.0535	1.105	-16.3252	6.054	-1.1614	30.6346	0.1237	-0.7266	0.5939	0.5991	-0.0963	-0.395	-0.1222	0.4599	-0.0274	-0.05	-0.0298	-0.0717	-0.0976	0.0026	0.0426	37.434	24.0253	24.6076
18	30.7247	-31.6071	3.9408	39.0739	-2.1843	4.9108	0.354	1.2234	-0.6347	-0.4731	-0.5013	0.6393	0.5009	-0.0034	0.1472	0.0047	0.0516	0.0265	0.0612	0.0316	-0.0429	2.714	23.1878	24.4778
19	3.0793	-0.7291	1.1963	3.2384	-2.3207	8.1176	0.0821	-0.049	-0.2001	0.132	-0.105	-0.2599	0.0815	0.1292	0.0229	-0.063	-0.0033	0.0129	-0.0738	0.0397	0.0474	36.3777	21.469	19.3838
20	1.7393	1.7417	-3.2222	5.2581	-3.7621	6.051	0.0208	0.1204	0.0003	0.1628	0.1144	0.1552	-0.0392	-0.229	-0.1352	-0.0582	0.0718	0.0197	0.0509	0.0496	-0.0289	4.0436	28.7087	25.3419

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 5
2	X-RAY DIFFRACTION	1	A	94 - 99
3	X-RAY DIFFRACTION	1	A	6 - 10
4	X-RAY DIFFRACTION	2	B	1 - 5
5	X-RAY DIFFRACTION	2	B	94 - 99
6	X-RAY DIFFRACTION	2	B	6 - 10
7	X-RAY DIFFRACTION	3	A	21 - 32
8	X-RAY DIFFRACTION	4	B	21 - 32
9	X-RAY DIFFRACTION	5	A	11 - 20
10	X-RAY DIFFRACTION	6	B	11 - 20
11	X-RAY DIFFRACTION	7	A	33 - 43
12	X-RAY DIFFRACTION	8	B	33 - 43
13	X-RAY DIFFRACTION	9	A	44 - 57
14	X-RAY DIFFRACTION	10	B	44 - 57
15	X-RAY DIFFRACTION	11	A	77 - 85
16	X-RAY DIFFRACTION	12	B	77 - 85
17	X-RAY DIFFRACTION	13	A	86 - 93
18	X-RAY DIFFRACTION	14	B	86 - 93
19	X-RAY DIFFRACTION	15	A	58 - 62
20	X-RAY DIFFRACTION	16	B	58 - 62
21	X-RAY DIFFRACTION	17	A	63 - 68
22	X-RAY DIFFRACTION	18	B	63 - 68
23	X-RAY DIFFRACTION	19	A	69 - 76
24	X-RAY DIFFRACTION	20	B	69 - 76

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