PDB-3saa: Crystal structure of Wild-type HIV-1 protease in complex With AF77

ID or keywords:

Entry

Database: PDB / ID: 3saa

Title

Crystal structure of Wild-type HIV-1 protease in complex With AF77

Components

Protease

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

aspartic-type endopeptidase activity / proteolysis
Similarity search - Function

Biological species

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

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

Citation

Journal: To be Published
Title: Protease Inhibitors that protrude out from substrate envelope are more susceptible to developing drug resistance
Authors: Altman, M.D. / Nalam, M.N.L. / Ali, A. / Cao, H. / Rana, T.M. / Schiffer, C.A. / Tidor, B.

History

Deposition	Jun 2, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 6, 2012	Provider: repository / Type: Initial release
Revision 1.1	Dec 12, 2012	Group: Other
Revision 1.2	Nov 8, 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	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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	3saa.cif.gz	100 KB	Display	PDBx/mmCIF format
PDB format	pdb3saa.ent.gz	78.4 KB	Display	PDB format
PDBx/mmJSON format	3saa.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3saa_validation.pdf.gz	757.7 KB	Display	wwPDB validaton report
Full document	3saa_full_validation.pdf.gz	759.6 KB	Display
Data in XML	3saa_validation.xml.gz	11.1 KB	Display
Data in CIF	3saa_validation.cif.gz	14.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sa/3saa ftp://data.pdbj.org/pub/pdb/validation_reports/sa/3saa	HTTPS FTP

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Related structure data

Related structure data	3sa3C 3sa4C 3sa5C 3sa6C 3sa7C 3sa8C 3sa9C 3sabC 3sacC 1f7aS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1t7i-d 2zga-1 3sa4-d 1mer-d 3em3-d 3oxv-2 3qbf-d 2qci-d 3sab-d 1ajv-d 1lzq-d 3o9d-d 1t7j-d 1mt9-d 3nu6-d 1hpo-d 6oy0-d 1d4k-d 4u7v-d 1qbt-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: Protease

B: Protease

hetero molecules

22.4 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)	51.007, 58.114, 61.971
Angle α, β, γ (deg.)	90.0, 90.0, 90.0
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 / Strain: HXB2 / Gene: gag-pol, pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106 / References: UniProt: O38732
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-77F / N-[(2S,3R)-4-{(cyclohexylmethyl)[(4-methoxyphenyl)sulfonyl]amino}-3-hydroxy-1-phenylbutan-2-yl]-3-hydroxybenzamide Type: Peptide-like / Class: Inhibitor / Mass: 566.708 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₁H₃₈N₂O₆S References: N-[(2S,3R)-4-{(CYCLOHEXYLMETHYL)[(4-METHOXYPHENYL)SULFONYL]AMINO}-3-HYDROXY-1-PHENYLBUTAN-2-YL]-3-HYDROXYBENZAMIDE
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 101 / 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: 42.06 %
Crystal grow	Temperature: 295 K / Method: hanging drop, vapor diffusion / pH: 6.2 Details: 24-29% ammonium sulfate, 63 mM sodium citrate, 126 mM phosphate buffer, pH 6.2, HANGING DROP, VAPOR DIFFUSION, temperature 295K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418

Detector

Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 14, 2009

Radiation

Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.95→50 Å / Num. obs: 12874 / % possible obs: 92.1 % / Redundancy: 6.9 % / R_merge(I) obs: 0.048 / Χ²: 1.007 / Net I/σ(I): 18.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.95-2.02	6.2	0.187	854	1.096	1	62.3
2.02-2.1	6.5	0.15	1182	1.023	1	87
2.1-2.2	7.2	0.128	1293	1.008	1	94.5
2.2-2.31	6.8	0.114	1313	1.055	1	94.7
2.31-2.46	7.3	0.089	1302	1.026	1	95.5
2.46-2.65	7.2	0.072	1334	0.988	1	95.8
2.65-2.91	7.1	0.056	1343	0.984	1	96.6
2.91-3.33	7.2	0.04	1369	1.03	1	97.9
3.33-4.2	6.6	0.032	1384	1.051	1	97
4.2-50	6.7	0.027	1500	0.863	1	98.6

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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 reduction
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F7A

1f7a

Resolution: 1.95→42.39 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.919 / WR_factor R_free: 0.2294 / WR_factor R_work: 0.1746 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.842 / SU B: 7.904 / SU ML: 0.113 / SU R Cruickshank DPI: 0.2017 / SU R_free: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.175 / 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	0.2281	638	5 %	RANDOM
R_work	0.1732	-	-	-
obs	0.1758	12798	91.84 %	-

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: 81.83 Å² / B_iso mean: 28.9368 Å² / B_iso min: 15.95 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.8 Å²	0 Å²	0 Å²
2-	-	0.11 Å²	0 Å²
3-	-	-	0.69 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→42.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1498	0	50	101	1649

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	1655
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1124
X-RAY DIFFRACTION	r_angle_refined_deg	1.474	2.017	2262
X-RAY DIFFRACTION	r_angle_other_deg	0.864	3	2772
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.132	5	211
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	43.734	24.915	59
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.878	15	282
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.121	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	263
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	1820
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	302
X-RAY DIFFRACTION	r_mcbond_it	0.577	1.5	1025
X-RAY DIFFRACTION	r_mcbond_other	0.173	1.5	428
X-RAY DIFFRACTION	r_mcangle_it	0.934	2	1674
X-RAY DIFFRACTION	r_scbond_it	1.648	3	630
X-RAY DIFFRACTION	r_scangle_it	2.471	4.5	588

LS refinement shell

Resolution: 1.95→2.001 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.175	29	-
R_work	0.157	563	-
all	-	592	-
obs	-	-	58.85 %

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	1.5885	1.8965	-2.1823	5.6326	-2.8499	4.3265	-0.2567	0.308	-0.074	-0.4524	0.1577	-0.0977	0.0971	-0.3014	0.099	0.1533	-0.0303	-0.0171	0.1156	-0.0329	0.0671	-4.9874	1.2968	-32.6679
2	18.5444	-0.7026	3.4563	1.6583	1.6547	2.8779	-0.0898	0.1564	-0.4047	-0.0147	-0.0183	0.0446	0.1915	-0.0278	0.1081	0.2059	-0.0202	0.0962	0.0721	-0.0021	0.1478	3.1333	-3.0159	-26.1925
3	0.8981	0.3326	1.6621	6.9176	6.9204	8.9269	0.0499	0.3813	0.1925	-0.0238	0.2226	-0.5955	0.0794	0.796	-0.2725	0.0779	-0.0055	0.0705	0.1862	0.0903	0.3539	16.8517	-2.0091	-22.961
4	6.8906	-2.5263	-1.9114	5.5596	0.3273	0.5616	-0.1296	0.0472	-0.2209	-0.0583	0.018	-0.1833	0.0627	-0.0143	0.1116	0.1553	0.0343	0.0602	0.1465	0.0223	0.0751	3.8808	-2.1072	-22.6148
5	1.5263	-1.5119	0.0604	2.1402	0.3897	2.0455	-0.0525	-0.2264	0.1591	0.1032	0.08	-0.1562	-0.0649	0.0188	-0.0275	0.0705	-0.0236	0.0005	0.0855	-0.0109	0.0534	0.2957	4.1022	-14.7967
6	10.7554	0.5326	0.9528	2.1658	0.629	0.3319	-0.0395	-0.1174	-0.3566	0.2982	-0.0175	-0.3133	0.1394	0.0157	0.0571	0.149	0.0247	0.0412	0.1213	0.0791	0.3055	11.5203	-6.0236	-13.1594
7	12.687	2.7275	-2.4535	10.2421	3.8623	2.4716	-0.1033	-0.9904	0.8051	-0.2834	0.4434	-0.1569	-0.1065	0.5257	-0.3401	0.0734	0.0227	-0.0218	0.343	-0.008	0.119	16.7244	1.0642	-6.934
8	5.8045	0.7078	3.6973	1.9278	1.57	4.7689	0.0324	-0.1983	0.2794	0.0223	-0.0941	0.1507	0.0804	-0.1271	0.0616	0.0767	-0.0186	0.0044	0.0558	0.003	0.0545	-0.6655	-1.099	-4.986
9	10.6637	3.3514	0.6529	1.865	-0.6738	4.2462	-0.0099	-0.1279	0.0051	0.2022	-0.0337	-0.0273	-0.0906	0.276	0.0436	0.095	-0.022	-0.0053	0.066	-0.0052	0.055	5.2702	-1.5557	-4.5237
10	3.184	-4.2841	0.9358	7.3417	-6.3068	16.4431	-0.1709	-0.1404	0.4189	0.3412	-0.0975	-0.6162	-0.4175	0.7953	0.2683	0.0481	-0.0798	-0.0325	0.2051	0.0379	0.1732	14.8983	6.2154	-12.5537
11	4.888	2.5113	1.1729	8.3103	-3.1579	12.4734	-0.0073	0.2585	-0.253	-0.4899	-0.1067	-0.1876	0.1156	0.2448	0.114	0.0695	0.0047	0.0541	0.079	-0.0041	0.1043	10.6313	5.4096	-26.6143
12	3.5097	0.42	-2.3401	2.6622	0.0076	7.5796	0.0613	-0.0159	0.2165	0.1002	-0.0271	-0.1078	-0.1518	0.1756	-0.0342	0.0157	-0.0275	-0.0175	0.0672	0.0257	0.1064	12.0322	8.1572	-18.0063
13	3.3979	2.1014	1.8289	3.8486	1.3899	4.7151	-0.0307	-0.2013	-0.065	0.0449	-0.0588	0.0908	0.2631	0.0086	0.0895	0.0599	0.0089	0.0085	0.0761	0.0264	0.0671	5.1035	-4.5741	-11.0517
14	0.2805	0.1152	-0.2824	0.0713	-0.352	2.6599	-0.0161	-0.011	-0.0782	-0.0019	-0.0409	-0.0303	0.0768	0.1158	0.057	0.095	-0.0231	0.0284	0.0853	-0.0056	0.088	2.2343	1.2132	-17.9437
15	4.1535	-0.5888	2.9906	0.8372	0.56	3.4385	0.0586	0.0343	0.1454	-0.0601	-0.0204	-0.1314	-0.0185	0.0029	-0.0382	0.0787	-0.0031	0.0167	0.0717	-0.0033	0.0933	5.1361	10.1307	-20.6059
16	3.2386	2.0995	2.9574	4.1966	2.282	3.618	-0.2819	-0.0649	0.1214	-0.1056	0.0737	0.3232	-0.2072	-0.2929	0.2082	0.1178	-0.0303	-0.0092	0.1272	0.0211	0.0733	-5.982	10.8277	-27.9211
17	5.3802	2.0631	-0.5404	2.3788	0.9563	1.7461	-0.1865	0.1407	0.4802	-0.2706	-0.0189	0.2661	-0.1857	-0.0855	0.2055	0.1587	-0.0296	-0.0697	0.0655	0.0399	0.1589	-4.9134	14.9042	-23.2788
18	27.7482	2.4043	6.8655	2.3224	1.7785	9.4585	0.2194	-0.8047	-0.5502	0.3919	0.0393	0.3155	0.1884	-0.104	-0.2587	0.0917	0.0061	0.0423	0.0495	0.0251	0.1165	-9.6652	11.2249	-16.3987
19	17.0336	6.6556	1.9396	3.775	3.4423	6.3601	0.0553	-0.0714	0.7933	0.0391	-0.3296	0.3842	0.0764	-0.7211	0.2743	0.0973	0.051	-0.0638	0.1831	0.0133	0.3206	-24.6566	6.9897	-19.057
20	14.0568	-6.1409	4.8966	5.8604	5.9355	22.2254	-0.6322	-1.9461	-0.1553	0.6046	0.4973	0.1646	0.7129	-1.4288	0.1349	0.16	0.0068	0.1246	0.3132	-0.0212	0.4321	-21.6384	8.0818	-14.7701
21	4.0677	1.5771	-1.4421	2.3473	0.6197	3.0969	0.0469	-0.0202	0.0998	-0.0566	0.1036	-0.0685	-0.0756	-0.0016	-0.1506	0.0478	-0.0112	-0.0185	0.0311	0.0076	0.0515	-8.711	1.2876	-20.6626
22	11.0684	0.082	-11.2524	1.5311	-0.1785	21.2143	-0.1063	-0.0075	-0.1178	0.147	0.0788	0.2593	0.1958	-0.2525	0.0275	0.0726	-0.0252	-0.0067	0.0369	0.0274	0.078	-17.593	-2.2293	-14.3509
23	9.8374	-3.9739	3.1313	8.1279	3.3321	4.2406	0.2097	-0.0233	-0.4742	-0.1977	-0.2657	0.5001	-0.0338	-0.2118	0.0559	0.1148	-0.0246	0.0191	0.1823	0.1002	0.1393	-25.1501	-8.9391	-14.5407
24	11.5812	10.8887	6.1598	10.5756	4.2711	10.5923	0.0272	-0.2409	-0.2239	0.0209	-0.1564	-0.2263	-0.2661	-0.1724	0.1292	0.0999	-0.0204	-0.0274	0.0954	0.038	0.081	-7.3417	-8.8871	-11.2072
25	7.0809	0.4421	2.6012	2.9184	-2.0395	3.5031	0.1684	-0.159	-0.0562	0.0091	0.0229	0.2975	0.139	-0.1678	-0.1914	0.0731	-0.0127	0.005	0.057	-0.0101	0.0673	-16.1557	-10.4916	-11.8827
26	10.2476	-4.9937	3.0888	20.8238	-7.7281	11.0786	0.1934	0.3014	-0.3257	-0.81	0.0405	0.4224	0.4044	0.1196	-0.2339	0.0468	-0.025	-0.0214	0.0688	0.0414	0.1386	-25.1224	-5.6447	-22.244
27	21.2975	5.7243	-14.4701	11.2043	-12.2077	17.0661	1.1291	0.0461	0.715	0.2061	-0.6071	0.17	-0.9168	0.4285	-0.522	0.5835	-0.0492	-0.1161	0.1251	0.1106	0.2624	-20.919	8.1504	-25.7873
28	5.0042	-0.4642	2.8407	12.6842	-6.8168	8.9673	-0.2716	0.1302	0.0902	0.1212	0.1588	0.1258	-0.0354	-0.1058	0.1128	0.0467	-0.0146	-0.0279	0.0548	0.0258	0.0793	-22.1886	-1.0424	-25.7306
29	5.1594	3.3346	-2.2206	4.4007	1.9457	6.5211	0.0217	-0.3226	-0.0758	0.0827	-0.1434	0.1348	-0.1843	0.2174	0.1217	0.177	0.003	0.0585	0.0688	0.0462	0.131	-16.3686	-3.5337	-10.8125
30	3.6381	-0.2698	-2.5363	4.2385	1.7622	5.2505	-0.0564	0.0541	0.2541	0.3667	0.1531	0.2888	0.2795	-0.0486	-0.0968	0.0643	-0.0102	0.0177	0.0229	0.02	0.0693	-12.7594	0.955	-18.6971
31	7.7907	6.6427	1.7503	11.7393	-5.1955	7.7561	-0.4288	0.5432	0.2682	-0.1919	0.5374	0.3886	-0.286	0.0531	-0.1086	0.0784	-0.0087	-0.0044	0.1972	0.0571	0.0711	-15.1303	1.0251	-28.1318
32	11.7305	4.285	1.8714	4.4426	-3.2229	5.8482	-0.058	0.1572	-0.0735	-0.2352	0.1511	-0.076	0.1732	-0.0558	-0.0931	0.1364	-0.0304	0.0256	0.0824	-0.0107	0.1206	-3.5796	7.321	-30.3929

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 - 52
9	X-RAY DIFFRACTION	9	A	53 - 58
10	X-RAY DIFFRACTION	10	A	59 - 63
11	X-RAY DIFFRACTION	11	A	64 - 69
12	X-RAY DIFFRACTION	12	A	70 - 75
13	X-RAY DIFFRACTION	13	A	76 - 81
14	X-RAY DIFFRACTION	14	A	82 - 87
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31	X-RAY DIFFRACTION	31	B	88 - 93
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