PDB-4qja: Crystal structure of inactive HIV-1 protease in complex with p1-p...

ID or keywords:

Entry

Database: PDB / ID: 4qja

Title

Crystal structure of inactive HIV-1 protease in complex with p1-p6 substrate variant (P453L)

Components

Protease
p1-p6 peptide

Keywords

HYDROLASE / co-evolution / protease

Function / homology

Function and homology information

viral budding via host ESCRT complex / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase ...
Similarity search - Function

Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...
Similarity search - Domain/homology

Biological species

Human immunodeficiency virus type 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.54 Å

Authors

Lin, K.H. / Schiffer, C.A.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease.
Authors: Ozen, A. / Lin, K.H. / Kurt Yilmaz, N. / Schiffer, C.A.

History

Deposition	Jun 3, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 29, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 26, 2014	Group: Database references
Revision 1.2	Dec 3, 2014	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4qja.cif.gz	102 KB	Display	PDBx/mmCIF format
PDB format	pdb4qja.ent.gz	81.6 KB	Display	PDB format
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Validation report

Summary document	4qja_validation.pdf.gz	452 KB	Display	wwPDB validaton report
Full document	4qja_full_validation.pdf.gz	452.5 KB	Display
Data in XML	4qja_validation.xml.gz	12.1 KB	Display
Data in CIF	4qja_validation.cif.gz	17 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qj/4qja ftp://data.pdbj.org/pub/pdb/validation_reports/qj/4qja	HTTPS FTP

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Related structure data

Related structure data	4qj2C 4qj6C 4qj7C 4qj8C 4qj9C C: citing same article (ref.)
Similar structure data	1msm-d 1mt8-d 2a1e-d 3gga-1 4obf-1 5ah6-d 4obg-1 3d1y-d 6pjh-d 1fg8-d 3sa6-d 1yt9-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 (1) #163 - Jul 2013 HIV Capsid similarity (3) #87 - Mar 2007 Zinc Fingers similarity (2)

Deposited unit

B: Protease

A: Protease

P: p1-p6 peptide

hetero molecules

23.2 kDa, 3 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)	51.007, 58.176, 61.774
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Protease / Retropepsin Mass: 10842.858 Da / Num. of mol.: 2 / Mutation: Q7K, D25N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 (ARV2/SF2 ISOLATE) Strain: HIV-1 M:B_ARV2/SF2 / Gene: gag-pol, pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): Tap106 / References: UniProt: P03369, HIV-1 retropepsin
#2: Protein/peptide	p1-p6 peptide Mass: 1189.368 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Human immunodeficiency virus type 1 (ARV2/SF2 ISOLATE) References: UniProt: P03349*PLUS
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 191 / 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 Å³/Da / Density % sol: 38.6 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: ammonium sulfate, sodium citrate, sodium phosphate, 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: 21-ID-F / Wavelength: 0.979 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 19, 2011
Radiation	Monochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.54→50 Å / Num. all: 195527 / Num. obs: 27160 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / R_sym value: 0.046 / Net I/σ(I): 37.02
Reflection shell	Resolution: 1.54→1.6 Å / Redundancy: 7 % / Mean I/σ(I) obs: 8 / R_sym value: 0.237 / % possible all: 94.1

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.8.0069	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.54→42.35 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.958 / SU B: 2.274 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17782	1372	5.1 %	RANDOM
R_work	0.15168	-	-	-
obs	0.15299	25755	97.17 %	-
all	-	195527	-	-

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: 19.701 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.4 Å²	0 Å²	-0 Å²
2-	-	0.36 Å²	-0 Å²
3-	-	-	0.04 Å²

Refinement step

Cycle: LAST / Resolution: 1.54→42.35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1575	0	15	191	1781

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	1817
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1816
X-RAY DIFFRACTION	r_angle_refined_deg	1.362	1.99	2492
X-RAY DIFFRACTION	r_angle_other_deg	0.706	3	4183
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.129	5	244
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.572	24.853	68
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.546	15	319
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.733	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	290
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	2113
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	390
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	0.586	0.965	937
X-RAY DIFFRACTION	r_mcbond_other	0.571	0.961	935
X-RAY DIFFRACTION	r_mcangle_it	0.969	1.445	1194
X-RAY DIFFRACTION	r_mcangle_other	0.969	1.447	1195
X-RAY DIFFRACTION	r_scbond_it	0.711	1.085	880
X-RAY DIFFRACTION	r_scbond_other	0.573	1.049	869
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	0.957	1.547	1281
X-RAY DIFFRACTION	r_long_range_B_refined	6.31	9.337	1932
X-RAY DIFFRACTION	r_long_range_B_other	6.318	9.342	1928
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.539→1.579 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.168	112	-
R_work	0.161	1797	-
obs	-	-	93.85 %

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	4.6797	4.7077	-2.5988	7.6524	-2.8118	5.6428	-0.1848	0.2131	-0.2664	-0.3019	0.0625	-0.2636	0.0832	-0.0961	0.1223	0.1161	-0.0062	-0.0039	0.0968	-0.0149	0.0456	-4.6933	1.6927	-32.7849
2	7.1701	1.4793	-0.2478	2.8812	-0.2468	0.0305	0.0602	0.2859	-0.2865	-0.2153	-0.0708	-0.0735	0.0388	0.0224	0.0105	0.1505	0.0441	0.0154	0.1295	-0.0222	0.0655	-0.5133	-4.0716	-27.103
3	8.1662	0.0235	3.9336	1.2042	0.9531	4.1441	0.0013	0.2109	0.0699	-0.1182	0.0088	-0.3039	0.0748	0.2626	-0.0101	0.0828	0.0087	0.0363	0.0955	0.0271	0.1355	15.2843	-1.0668	-22.6816
4	14.7162	-5.1646	-0.4136	4.0837	0.0486	1.4085	-0.0323	-0.0118	-0.3382	-0.1595	-0.0294	-0.1162	0.1663	0.009	0.0617	0.1454	0.0282	0.0301	0.075	0.0083	0.0651	6.9325	-3.1753	-23.2884
5	1.7576	0.9488	0.867	2.3435	-0.2461	5.3863	0.068	-0.0982	-0.0477	0.1241	0.0379	-0.1249	0.0662	0.1159	-0.1059	0.065	0.0012	-0.0085	0.0468	-0.0124	0.0469	-1.7071	4.8533	-15.863
6	7.5522	-7.2386	0.3246	19.4865	-3.2843	2.7552	-0.0921	-0.1106	-0.3124	0.1436	-0.0428	-0.1007	0.1155	0.1282	0.135	0.0623	-0.0088	-0.0009	0.0866	0.0043	0.062	7.6879	-3.3668	-13.5955
7	6.1905	3.7611	1.6188	7.0883	6.0108	8.3356	-0.0929	-0.2729	0.0678	-0.06	0.0691	-0.0734	-0.1404	0.5226	0.0238	0.039	0.0109	-0.0117	0.1514	0.043	0.1049	17.6713	-1.095	-10.7041
8	8.9692	0.6526	-1.8585	2.9253	-1.191	2.9341	0.002	-0.4186	0.2875	0.1287	-0.0918	-0.1952	-0.0208	0.3922	0.0898	0.0774	-0.0081	-0.0153	0.1075	-0.0216	0.0473	8.1778	1.6833	-2.7961
9	7.5902	3.1995	3.4541	4.8695	2.3206	4.3162	0.0128	-0.0918	0.0203	0.1353	0.0108	0.1809	0.0101	-0.2301	-0.0235	0.0792	-0.0102	0.0136	0.0694	0.0123	0.033	-4.2276	-2.913	-6.0517
10	10.1955	7.5856	-5.713	6.9396	-6.0693	5.8142	-0.051	-0.0892	-0.0534	0.0489	-0.1587	-0.1876	-0.0155	0.2547	0.2097	0.1406	0.0423	-0.0427	0.1645	-0.0255	0.0872	10.0306	0.1977	-5.9404
11	2.3399	1.1299	-0.4746	5.2054	0.5163	9.7567	0.0668	-0.2476	0.014	0.1926	-0.162	-0.2337	-0.1835	0.1394	0.0952	0.0729	0.0016	-0.0024	0.1232	0.0089	0.1457	14.6764	7.6847	-14.9169
12	8.2472	2.4152	2.0548	10.9128	-2.1415	9.6414	-0.0199	0.689	-0.1313	-0.3012	0.1806	-0.4728	-0.2498	0.4501	-0.1607	0.0808	0.0173	0.0479	0.0989	-0.0017	0.1079	11.3062	6.4667	-27.1482
13	1.2497	1.7251	-2.3189	4.8034	-3.5674	4.3742	0.0433	-0.116	0.0078	0.0904	-0.0838	-0.2107	-0.056	0.1785	0.0405	0.0618	-0.0168	-0.0278	0.1008	-0.0026	0.119	10.2337	4.5346	-13.382
14	1.9822	1.4518	0.8127	5.8446	-4.3213	5.8609	0.0525	-0.0399	-0.0917	-0.0334	0.0004	0.13	0.2535	-0.097	-0.0529	0.1006	0.0094	0.0381	0.0704	0.0022	0.1143	3.169	-5.488	-14.8346
15	1.7073	1.0564	-0.0427	3.0974	-0.6008	2.0578	-0.0254	0.0505	0.1534	-0.1069	0.0041	-0.1886	-0.0147	0.1161	0.0212	0.0575	-0.0015	0.0048	0.0586	0.0055	0.0703	3.8886	9.2049	-20.1458
16	12.4853	4.5104	4.698	4.2128	0.3692	6.9813	-0.0994	-0.0561	0.1663	-0.1343	0.023	0.1752	-0.146	-0.1787	0.0764	0.0995	0.0004	-0.0077	0.0638	-0.006	0.0584	-6.8729	10.4744	-28.1109
17	2.4165	3.1058	3.3986	4.8136	2.8186	7.7173	-0.2856	-0.0647	0.2029	-0.4076	0.0418	0.2703	-0.3477	-0.3091	0.2439	0.127	0.0123	-0.0241	0.0564	-0.0086	0.0925	-5.0732	14.734	-23.4691
18	11.4354	1.1712	1.6237	0.8992	0.4752	1.8038	-0.0014	-0.2273	0.2165	0.1092	-0.0145	0.0432	-0.0704	-0.0561	0.0159	0.0847	0.0046	0.0087	0.0503	-0.0048	0.088	-12.0598	10.8413	-17.0372
19	1.4982	1.6835	2.3584	6.2859	8.4427	11.3504	0.1942	-0.0451	-0.2232	0.2678	-0.4432	0.2112	0.3703	-0.6135	0.249	0.1177	-0.0353	0.0565	0.2973	0.0881	0.3051	-26.8052	6.5603	-17.7906
20	10.2053	-2.9954	-3.7534	2.0069	1.747	3.6206	-0.0523	-0.2349	0.1304	0.1593	0.0921	0.0579	-0.0588	-0.0245	-0.0397	0.0835	-0.0024	0.0059	0.0559	0.0093	0.0678	-14.2519	6.4823	-17.3538
21	5.2695	0.3007	-2.2502	1.7606	0.5363	2.4396	-0.0639	0.026	-0.2125	0.0274	0.0526	0.1259	0.214	-0.0595	0.0114	0.0808	-0.0077	-0.007	0.0543	0.0048	0.0568	-10.7308	-2.9891	-20.2654
22	13.2946	0.2636	-3.5584	3.8235	0.2207	8.4035	0.1312	-0.2916	0.1691	0.0392	0.0019	0.2196	0.0153	-0.2091	-0.133	0.0829	0.0071	0.0024	0.0746	0.0063	0.0632	-22.6236	-0.7958	-10.7465
23	8.9251	-5.971	-0.5146	6.9563	2.6752	2.891	0.0633	0.1262	-0.2928	0.0024	-0.1368	0.3884	-0.0423	-0.2891	0.0734	0.061	-0.0121	-0.0189	0.0864	0.0473	0.1209	-26.6872	-10.4394	-15.4459
24	10.3258	5.5729	2.0227	5.1703	1.396	0.4528	-0.097	0.1087	-0.0051	-0.0523	0.0661	0.083	-0.0092	0.0416	0.0309	0.085	-0.001	0.0044	0.0795	0.0043	0.0531	-9.1712	-9.471	-12.351
25	8.7704	-0.2319	3.1704	1.4931	-1.1289	1.8808	0.0869	-0.1217	-0.0535	-0.0263	0.0245	0.1348	0.0486	-0.0547	-0.1113	0.075	-0.0052	0.0066	0.0613	-0.0048	0.0755	-15.5392	-10.191	-11.5461
26	2.6996	-0.8807	0.5915	9.1926	-8.236	8.7121	0.0879	0.1557	-0.2246	-0.4024	0.0397	0.1174	0.2884	-0.0523	-0.1276	0.0612	-0.0169	-0.0246	0.1031	0.0163	0.1183	-24.9487	-5.7235	-22.344
27	9.8204	3.9714	-5.9875	6.0486	-2.3423	11.139	0.0784	-0.1687	0.2318	-0.0512	-0.0525	0.1203	-0.2177	-0.1733	-0.0259	0.0888	-0.0162	-0.0466	0.0775	0.0027	0.0764	-20.5226	7.6608	-26.1281
28	2.1963	-0.7464	2.4245	4.5811	-4.892	6.5112	-0.0232	-0.007	0.0402	0.0157	0.0956	0.1209	-0.0202	-0.1252	-0.0724	0.0719	-0.0068	-0.0031	0.102	-0.0003	0.0925	-22.0402	-1.2454	-25.8582
29	2.7842	0.4642	-2.8968	3.5785	-2.0532	3.7221	0.0757	-0.2214	-0.1001	0.2995	-0.1629	0.0174	-0.2242	0.2717	0.0872	0.1038	-0.004	0.0171	0.1011	0.0124	0.0833	-16.5399	-3.2438	-10.9274
30	3.1531	-1.1603	-3.599	3.9525	2.2844	6.5967	0.0591	-0.1112	0.1001	0.101	0.048	0.1224	-0.0727	0.0947	-0.1071	0.0572	-0.0172	-0.0029	0.064	0.0128	0.0572	-12.7736	1.0136	-18.7513
31	2.8221	-0.2224	2.3433	6.4345	-1.6046	2.2616	-0.1444	0.1233	0.0881	-0.1019	0.1272	0.2516	-0.0894	0.0589	0.0172	0.0944	-0.0205	-0.0143	0.144	0.0104	0.0514	-14.6611	1.0505	-28.52
32	10.6065	2.4381	1.0262	3.8967	-0.827	3.8249	-0.0369	0.1795	-0.0133	-0.1599	0.0463	-0.1374	-0.0214	0.1401	-0.0094	0.0955	-0.0042	0.0064	0.0706	-0.0053	0.0617	-2.5225	7.3303	-30.1739

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 - 11
3	X-RAY DIFFRACTION	3	A	12 - 18
4	X-RAY DIFFRACTION	4	A	19 - 24
5	X-RAY DIFFRACTION	5	A	25 - 30
6	X-RAY DIFFRACTION	6	A	31 - 35
7	X-RAY DIFFRACTION	7	A	36 - 41
8	X-RAY DIFFRACTION	8	A	42 - 47
9	X-RAY DIFFRACTION	9	A	48 - 54
10	X-RAY DIFFRACTION	10	A	55 - 59
11	X-RAY DIFFRACTION	11	A	60 - 64
12	X-RAY DIFFRACTION	12	A	65 - 70
13	X-RAY DIFFRACTION	13	A	71 - 78
14	X-RAY DIFFRACTION	14	A	79 - 84
15	X-RAY DIFFRACTION	15	A	85 - 94
16	X-RAY DIFFRACTION	16	A	95 - 99
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