PDB-4djr: Crystal Structure of wild-type HIV-1 Protease in Complex with MKP97

ID or keywords:

Entry

Database: PDB / ID: 4djr

Title

Crystal Structure of wild-type HIV-1 Protease in Complex with MKP97

Components

Pol polyprotein

Keywords

HYDROLASE/HYDROLASE inhibitor / HIV-1 protease / drug resistance / drug design / Protease inhibitors / AIDS / Aspartyl protease / HYDROLASE-HYDROLASE inhibitor complex

Function / homology

Function and homology information

viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / endonuclease activity / aspartic-type endopeptidase activity / proteolysis / DNA binding
Similarity search - Function

Biological species

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

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

Citation

Journal: J.Med.Chem. / Year: 2012
Title: Design, synthesis, and biological and structural evaluations of novel HIV-1 protease inhibitors to combat drug resistance.
Authors: Parai, M.K. / Huggins, D.J. / Cao, H. / Nalam, M.N. / Ali, A. / Schiffer, C.A. / Tidor, B. / Rana, T.M.

History

Deposition	Feb 2, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 1, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 2, 2013	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software
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	4djr.cif.gz	101.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4djr.ent.gz	80.7 KB	Display	PDB format
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Validation report

Summary document	4djr_validation.pdf.gz	769.8 KB	Display	wwPDB validaton report
Full document	4djr_full_validation.pdf.gz	771 KB	Display
Data in XML	4djr_validation.xml.gz	12.2 KB	Display
Data in CIF	4djr_validation.cif.gz	17.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dj/4djr ftp://data.pdbj.org/pub/pdb/validation_reports/dj/4djr	HTTPS FTP

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Related structure data

Related structure data	4djoC 4djpC 4djqC C: citing same article (ref.)
Similar structure data	6oxz-d 4djp-d 6oxt-d 4f76-d 3sab-d 4njt-1 1d4k-d 2psv-d 1lzq-d 2nxl-d 4mc1-d 3o9d-d 6opu-d 1g2k-d 4mc6-d 4q1y-d 2qhy-d 1npv-d 2i0a-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 (1)

Deposited unit

A: Pol polyprotein

B: Pol polyprotein

hetero molecules

22.5 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)	50.728, 57.850, 61.692
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Pol polyprotein / HIV-1 Protease Mass: 10815.790 Da / Num. of mol.: 2 / Fragment: unp residues 1-99 / Mutation: Q7K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: SF2 / Gene: gag-pol, pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP56 / References: UniProt: Q90K99
#2: Chemical	ChemComp-0KJ / [(2S)-5-oxopyrrolidin-2-yl]methyl [(2S,3R)-4-{(1,3-benzothiazol-6-ylsulfonyl)[(2S)-2-methylbutyl]amino}-3-hydroxy-1-phenylbutan-2-yl]carbamate Mass: 588.739 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₈H₃₆N₄O₆S₂
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.09 Å³/Da / Density % sol: 41.21 %
Crystal grow	Temperature: 295 K / pH: 6.2 Details: 126mM Phosphate buffer, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, pH 6.2, temperature 295K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

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

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2010

Radiation

Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9 Å / Relative weight: 1

Reflection

Resolution: 1.55→50 Å / Num. obs: 26519 / % possible obs: 97.9 % / Redundancy: 6.4 % / R_merge(I) obs: 0.056 / Χ²: 1.137 / Net I/σ(I): 14.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.55-1.61	3.8	0.346	2283	1.117	1	85.6
1.61-1.67	4.6	0.303	2532	1.189	1	94.7
1.67-1.75	6.3	0.259	2644	1.312	1	99.6
1.75-1.84	7.1	0.187	2655	1.295	1	100
1.84-1.95	7.1	0.125	2682	1.28	1	100
1.95-2.1	7.1	0.086	2690	1.177	1	99.9
2.1-2.32	7.1	0.07	2691	1.062	1	100
2.32-2.65	7.1	0.057	2724	0.947	1	100
2.65-3.34	6.9	0.053	2749	1.156	1	100
3.34-50	6.4	0.033	2869	0.856	1	99.2

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.55→39.18 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.956 / WR_factor R_free: 0.206 / WR_factor R_work: 0.1794 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.871 / SU B: 3.423 / SU ML: 0.058 / SU R Cruickshank DPI: 0.0856 / SU R_free: 0.0835 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1964	1319	5 %	RANDOM
R_work	0.1701	-	-	-
obs	0.1715	26380	97.65 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 78.69 Å² / B_iso mean: 22.543 Å² / B_iso min: 9.4 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.74 Å²	0 Å²	0 Å²
2-	-	-0.01 Å²	0 Å²
3-	-	-	0.76 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→39.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1502	0	55	180	1737

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	1648
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1110
X-RAY DIFFRACTION	r_angle_refined_deg	1.393	2.021	2254
X-RAY DIFFRACTION	r_angle_other_deg	0.83	3	2744
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.014	5	210
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.277	25	56
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.966	15	282
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.868	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	264
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	1801
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	295
X-RAY DIFFRACTION	r_mcbond_it	0.589	1.5	1020
X-RAY DIFFRACTION	r_mcbond_other	0.169	1.5	426
X-RAY DIFFRACTION	r_mcangle_it	1.011	2	1668
X-RAY DIFFRACTION	r_scbond_it	1.639	3	628
X-RAY DIFFRACTION	r_scangle_it	2.561	4.5	586

LS refinement shell

Resolution: 1.55→1.59 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.282	83	-
R_work	0.22	1569	-
all	-	1652	-
obs	-	-	84.2 %

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	2.3784	-0.0126	0.1615	3.8185	-2.0847	5.2657	-0.1415	-0.3301	0.1302	0.4062	0.1607	-0.0501	-0.2313	-0.1758	-0.0192	0.1784	0.0253	0.0155	0.1195	-0.0121	0.0371	20.4784	27.8139	32.4279
2	14.6538	0.8353	0.0309	2.6418	-0.2528	0.0307	-0.1601	-0.206	0.4576	0.6726	0.0946	-0.1325	-0.0876	-0.0069	0.0655	0.268	0.0058	-0.133	0.0795	-0.0074	0.1458	28.5515	32.0131	25.8746
3	0.3767	-1.3649	-1.6119	8.2183	4.1224	7.8274	-0.0403	-0.0698	0.0869	0.4895	-0.1033	-1.4022	-0.1491	0.4724	0.1435	0.0604	-0.0466	-0.1331	0.0912	0.1074	0.4223	42.14	30.7967	22.3507
4	7.6104	3.9165	-0.1811	8.4491	-1.5059	0.4084	-0.0716	-0.0157	0.2531	0.4418	-0.0664	-0.211	-0.1981	0.0887	0.138	0.1724	-0.0436	-0.0849	0.1151	0.0371	0.0977	29.2677	31.0207	22.2871
5	9.3836	3.2384	-1.6252	2.8258	-1.6252	0.9479	-0.1204	0.5572	-0.217	-0.2393	0.1065	-0.0387	0.1282	-0.0398	0.0139	0.1081	0.0085	0.005	0.0879	-0.0092	0.0589	25.6297	24.6107	14.6481
6	9.4359	-1.067	-1.0535	2.7274	-0.3912	3.2508	-0.0639	0.238	0.4145	-0.2345	-0.1827	-0.4426	-0.2847	0.2559	0.2466	0.0893	-0.0217	0.003	0.1121	0.0572	0.1368	36.6711	34.6587	12.7007
7	15.2097	-2.9441	1.8556	6.6322	5.0911	5.1273	0.0447	0.6503	-0.4287	-0.1922	0.4452	-0.4037	-0.1559	0.6108	-0.49	0.0591	-0.0084	0.0415	0.2222	0.0158	0.109	41.9439	27.5303	6.7985
8	11.2231	-3.4753	-7.3053	3.366	3.1381	8.7588	-0.2601	0.1196	-0.6129	0.0353	-0.0086	0.2193	0.2172	0.0771	0.2687	0.1193	0.022	-0.0057	0.0836	-0.0074	0.1049	26.2137	28.5253	4.4853
9	9.5476	-2.0314	0.1368	2.4067	-0.189	2.7531	-0.0214	0.1585	-0.1689	-0.2177	0.028	0.1958	-0.0685	-0.0392	-0.0066	0.1066	0.0099	-0.0102	0.0901	-0.012	0.0706	25.7733	32.0928	3.647
10	6.7975	-5.6902	2.5486	9.5525	-9.7935	13.2321	0.1527	0.3655	-0.3078	-0.1094	-0.425	0.0263	0.0545	0.406	0.2723	0.0858	0.0468	0.0474	0.1835	0.009	0.1329	37.6447	25.9889	7.6419
11	7.4546	-2.4634	-0.0632	7.4028	0.4524	9.6165	0.0754	0.0252	0.3752	0.1012	-0.2481	-0.7721	0.0489	0.2878	0.1727	0.0374	-0.0136	-0.0234	0.1033	0.0623	0.1888	39.8795	22.3393	18.5517
12	7.3429	1.0337	-1.0608	7.3302	-0.2617	6.9946	-0.0953	-0.4303	0.1912	0.6542	-0.0307	-0.2703	0.0252	0.2872	0.126	0.1215	0.0032	-0.0595	0.0825	0.0069	0.1102	35.9236	21.846	26.7334
13	0.9145	-0.274	1.3821	1.9233	-0.8023	2.1867	-0.0451	0.0927	0.0138	-0.1886	-0.0311	-0.077	-0.0185	0.1269	0.0762	0.0747	0.0093	0.0391	0.1105	0.0131	0.1139	33.6631	27.5629	11.9817
14	0.6655	1.8114	-1.1666	9.3727	-1.714	2.5309	0.0459	-0.0173	0.0516	-0.1814	-0.0214	0.266	-0.1829	0.044	-0.0245	0.0858	0.0023	-0.0199	0.079	0.0135	0.1098	28.0544	31.373	17.3619
15	2.0485	-1.5499	-0.596	3.1188	-0.9342	2.8929	0.019	-0.0561	-0.049	0.0804	-0.029	-0.0336	0.0688	0.1213	0.0099	0.0611	0.006	-0.002	0.0616	0.0024	0.0719	29.2741	18.7387	20.2889
16	7.7159	-1.85	-4.1287	1.874	0.642	4.8573	-0.1982	0.0925	-0.2475	0.1049	0.1263	0.2021	0.2628	-0.2811	0.0719	0.1249	0.0159	0.0231	0.097	0.0304	0.0735	18.5225	18.3894	28.0502
17	1.8837	-1.4396	-2.1	3.5209	0.3119	5.0324	-0.0761	-0.0159	-0.2991	0.337	-0.0241	0.1972	0.1508	-0.1533	0.1002	0.1251	-0.0004	0.012	0.0847	0.0009	0.1165	20.4651	14.0845	23.3916
18	13.4	-1.5731	-0.9222	0.4879	0.961	2.5286	-0.0464	0.1121	-0.363	0.0348	-0.0152	0.0963	0.1415	-0.0236	0.0616	0.1099	-0.0205	-0.0453	0.0545	0.0196	0.2308	13.104	18.0851	17.123
19	17.1534	-11.7237	0.355	39.1555	33.1988	35.9184	1.1519	-0.8659	-1.8481	-1.1507	-1.3396	1.3372	-0.4839	-2.2646	0.1877	0.0993	0.0256	-0.0177	0.2981	0.1238	0.5819	-1.2065	22.8302	17.8677
20	5.9959	2.0364	2.3987	2.7237	0.361	3.868	0.0307	-0.0029	-0.4372	-0.3535	0.1514	0.2826	0.167	-0.1476	-0.182	0.1005	-0.0037	-0.0463	0.0584	0.0249	0.1922	11.1088	22.427	17.1928
21	6.2436	-2.4078	3.383	3.1238	-1.8118	2.537	-0.1537	0.024	0.0879	0.1182	0.1238	0.1821	-0.2139	-0.0398	0.0299	0.0882	0.0124	0.0243	0.0757	0.0096	0.0642	14.6515	31.8873	20.219
22	14.6867	-2.3175	1.64	7.0476	1.456	7.2594	0.2675	0.2266	-0.2559	-0.3109	-0.0995	0.0804	0.2414	-0.5141	-0.1681	0.0972	-0.0079	-0.0159	0.1255	0.0257	0.0702	2.6238	30.3334	10.5661
23	11.6687	4.9784	-0.5678	3.7702	2.6591	5.9645	0.331	0.4791	0.4517	0.184	0.0126	0.1795	-0.1114	-0.5762	-0.3436	0.0635	0.0531	0.0556	0.0983	0.0982	0.1448	0.8303	39.6676	15.1784
24	12.8111	-7.9712	-0.2573	7.3147	1.5038	2.7836	-0.1119	-0.173	-0.1196	0.0222	0.0162	0.0816	-0.0549	0.0821	0.0956	0.0896	-0.0042	0.0153	0.0672	0.003	0.062	16.4535	38.8037	11.8446
25	13.0714	-1.7451	1.3528	3.7451	-2.0044	1.0874	0.1671	0.4199	-0.0361	-0.1717	-0.1127	0.1089	0.0942	0.0674	-0.0544	0.0964	0.0079	-0.0108	0.1112	-0.0289	0.0862	13.8802	39.2692	9.351
26	4.352	4.8481	-5.0267	8.7766	-3.82	8.4401	0.1508	-0.0276	0.2899	0.2299	0.1961	0.4007	-0.2161	-0.0737	-0.3469	0.0461	0.0457	0.0236	0.1093	0.0559	0.1914	1.5184	35.9287	19.8262
27	19.8747	-6.0779	17.2273	5.3353	-11.3122	27.8818	0.2189	0.0028	-0.4997	0.3022	0.0702	0.4151	0.1837	-0.3937	-0.2892	0.262	0.0211	0.2618	0.1349	0.0553	0.3034	4.7139	21.2463	25.7857
28	1.1724	1.3679	-1.8134	4.7327	-2.8169	3.9184	-0.1125	-0.1275	0.033	-0.0491	0.1194	0.0285	0.1236	-0.0783	-0.007	0.0691	0.0454	0.0467	0.1192	0.0561	0.1509	3.3178	30.1575	25.5419
29	3.8755	-2.0861	2.176	2.0128	-0.3121	13.4292	0.0404	0.4185	-0.0094	-0.225	-0.1009	0.1931	0.4587	0.3441	0.0605	0.1071	-0.0021	-0.0162	0.0934	0.0343	0.1271	9.0218	32.3548	10.639
30	2.567	-0.9571	1.7229	3.7551	0.2792	4.2074	0.0492	0.0518	-0.2268	-0.129	0.1262	0.3201	-0.0431	-0.0185	-0.1754	0.0791	0.0132	0.0002	0.0736	0.0242	0.1067	12.3365	28.2746	18.5975
31	6.9812	-4.104	-2.2142	6.8245	3.8545	2.223	-0.6624	-0.5427	-0.4301	0.388	0.4178	0.5362	0.1376	0.163	0.2446	0.196	0.1343	0.1365	0.1819	0.1183	0.1433	10.3476	27.3119	28.5786
32	14.7017	-5.8403	-2.7274	6.401	-1.7464	4.1379	-0.1807	-0.4599	0.1927	0.4293	0.2164	-0.0767	-0.062	0.0676	-0.0358	0.1393	0.0247	0.0107	0.1033	0.0037	0.0682	21.8955	21.8301	30.3312

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 7
2	X-RAY DIFFRACTION	2	A	8 - 13
3	X-RAY DIFFRACTION	3	A	14 - 19
4	X-RAY DIFFRACTION	4	A	20 - 25
5	X-RAY DIFFRACTION	5	A	26 - 32
6	X-RAY DIFFRACTION	6	A	33 - 37
7	X-RAY DIFFRACTION	7	A	38 - 43
8	X-RAY DIFFRACTION	8	A	44 - 50
9	X-RAY DIFFRACTION	9	A	51 - 56
10	X-RAY DIFFRACTION	10	A	57 - 60
11	X-RAY DIFFRACTION	11	A	61 - 65
12	X-RAY DIFFRACTION	12	A	66 - 71
13	X-RAY DIFFRACTION	13	A	72 - 80
14	X-RAY DIFFRACTION	14	A	81 - 86
15	X-RAY DIFFRACTION	15	A	87 - 94
16	X-RAY DIFFRACTION	16	A	95 - 99
17	X-RAY DIFFRACTION	17	B	1 - 6
18	X-RAY DIFFRACTION	18	B	7 - 13
19	X-RAY DIFFRACTION	19	B	14 - 19
20	X-RAY DIFFRACTION	20	B	20 - 25
21	X-RAY DIFFRACTION	21	B	26 - 32
22	X-RAY DIFFRACTION	22	B	33 - 37
23	X-RAY DIFFRACTION	23	B	38 - 45
24	X-RAY DIFFRACTION	24	B	46 - 50
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