PDB-3sa7: Crystal structure of wild-type HIV-1 protease in complex with AF55

ID or keywords:

Entry

Database: PDB / ID: 3sa7

Title

Crystal structure of wild-type HIV-1 protease in complex with AF55

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 /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 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	3sa7.cif.gz	96.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3sa7.ent.gz	74.9 KB	Display	PDB format
PDBx/mmJSON format	3sa7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3sa7_validation.pdf.gz	736.7 KB	Display	wwPDB validaton report
Full document	3sa7_full_validation.pdf.gz	738.2 KB	Display
Data in XML	3sa7_validation.xml.gz	6.6 KB	Display
Data in CIF	3sa7_validation.cif.gz	9.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sa/3sa7 ftp://data.pdbj.org/pub/pdb/validation_reports/sa/3sa7	HTTPS FTP

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Related structure data

Related structure data	3sa3C 3sa4C 3sa5C 3sa6C 3sa8C 3sa9C 3saaC 3sabC 3sacC 1f7aS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3mxe-d 1t7j-d 3o9i-d 4q1x-d 6oy1-d 2psv-d 2nxl-d 6pje-d 1mer-d 2pqz-d 4tvg-d 1bv9-d 2qi1-d 1meu-d 1k6c-d 6dh7-d 4dqh-d 4njs-2 3mxd-d 4njt-1 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)	50.922, 57.764, 61.649
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
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-55A / N~2~-acetyl-N-[(2S,3R)-4-{(1,3-benzothiazol-6-ylsulfonyl)[(2S)-2-methylbutyl]amino}-3-hydroxy-1-phenylbutan-2-yl]-L-leucinamide Type: Peptide-like / Class: Inhibitor / Mass: 602.808 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₀H₄₂N₄O₅S₂ References: N~2~-ACETYL-N-[(2S,3R)-4-{(1,3-BENZOTHIAZOL-6-YLSULFONYL)[(2S)-2-METHYLBUTYL]AMINO}-3-HYDROXY-1-PHENYLBUTAN-2-YL]-L-LEUCINAMIDE
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 161 / 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: 41.31 %
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:

SYNCHROTRON / Site:

APS

/ Beamline: 14-ID-B / Wavelength: 0.9002

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 16, 2009

Radiation

Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9002 Å / Relative weight: 1

Reflection

Resolution: 1.5→50 Å / Num. obs: 29808 / % possible obs: 99.8 % / Redundancy: 7 % / R_merge(I) obs: 0.068 / Χ²: 1.032 / Net I/σ(I): 10.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.5-1.55	7.1	0.428	2922	1.064	1	100
1.55-1.62	7.1	0.288	2957	0.99	1	100
1.62-1.69	7.1	0.228	2934	1.007	1	100
1.69-1.78	7.1	0.172	2947	1.065	1	100
1.78-1.89	7.1	0.131	2960	1.024	1	100
1.89-2.04	7.1	0.108	2953	1.058	1	100
2.04-2.24	7	0.081	2986	1.037	1	100
2.24-2.56	7	0.075	2997	1.014	1	100
2.56-3.23	6.8	0.063	3038	1.032	1	100
3.23-50	6.3	0.032	3114	1.028	1	97.8

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F7A

1f7a

Resolution: 1.5→42.15 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.936 / WR_factor R_free: 0.2311 / WR_factor R_work: 0.1978 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8494 / SU B: 3.143 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0866 / SU R_free: 0.0883 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2317	1504	5.1 %	RANDOM
R_work	0.197	-	-	-
obs	0.1987	29673	99.44 %	-

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: 30.38 Å² / B_iso mean: 17.438 Å² / B_iso min: 2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.46 Å²	0 Å²	0 Å²
2-	-	-0.1 Å²	0 Å²
3-	-	-	0.56 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→42.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1494	0	51	161	1706

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	1626
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1081
X-RAY DIFFRACTION	r_angle_refined_deg	1.481	2.018	2226
X-RAY DIFFRACTION	r_angle_other_deg	0.824	3	2671
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.249	5	208
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.574	25	56
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.062	15	270
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.587	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	264
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	1787
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	293
X-RAY DIFFRACTION	r_mcbond_it	0.508	1.5	1014
X-RAY DIFFRACTION	r_mcbond_other	0.161	1.5	424
X-RAY DIFFRACTION	r_mcangle_it	0.83	2	1655
X-RAY DIFFRACTION	r_scbond_it	1.435	3	612
X-RAY DIFFRACTION	r_scangle_it	2.166	4.5	571

LS refinement shell

Resolution: 1.499→1.538 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.436	116	-
R_work	0.346	2022	-
all	-	2138	-
obs	-	-	98.21 %

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	2.3163	-0.4875	0.1352	4.5971	-0.4445	3.2236	-0.1515	-0.3465	0.0729	0.4234	0.1283	-0.07	-0.1509	-0.0084	0.0233	0.1471	0.0325	0.0069	0.1207	-0.0082	0.0428	21.1835	26.0109	29.5754
2	3.0917	-1.0072	-0.4353	4.8284	0.555	3.7593	-0.0726	-0.0417	-0.2366	0.2007	0.1256	0.2692	0.279	-0.2469	-0.053	0.089	0.0025	0.0168	0.0698	0.021	0.0812	19.7387	17.3274	22.9246
3	7.4083	1.8629	1.0836	4.6121	-1.0425	2.0971	-0.0731	0.0133	0.1004	-0.0337	-0.0645	-0.138	-0.124	0.1493	0.1376	0.045	0.01	-0.0044	0.0326	0.0155	0.0147	27.9786	28.0738	18.4737
4	7.6874	0.2876	1.809	4.1225	-1.1623	2.1737	-0.0156	0.1648	-0.3176	-0.1091	0.204	0.3625	0.016	-0.1271	-0.1884	0.062	0.0056	0.0074	0.0562	0.0251	0.0557	12.4068	26.8766	18.5411
5	13.1219	0.6759	-5.1517	5.6234	3.4301	4.5695	0.6621	-1.127	-1.1114	0.3173	-0.4205	-1.2888	-0.2301	0.3047	-0.2417	0.2917	-0.1726	-0.3572	0.261	0.2803	0.6	39.8592	30.566	23.952
6	22.5263	-10.9896	-0.4209	6.3443	0.5626	3.8805	0.3524	-0.0463	-1.0834	-0.2356	-0.0911	0.9592	0.016	-0.8163	-0.2613	0.1185	-0.019	-0.0012	0.2255	0.0472	0.4231	1.0082	21.3689	18.2961
7	5.2952	-0.1559	-0.2798	2.0022	1.785	5.6268	-0.0479	0.1486	0.2333	-0.0976	0.1981	-0.4439	-0.1202	0.7198	-0.1502	0.1095	-0.022	0.0071	0.1864	0.0563	0.1718	39.5856	31.3611	10.1726
8	7.2022	-2.3637	-2.6295	8.4441	3.6999	4.2537	0.1325	0.3957	-0.0568	0.0776	-0.1419	0.5333	0.0536	-0.6558	0.0094	0.1074	0.0139	0.0013	0.2292	0.0815	0.1359	0.4525	34.1247	13.1346
9	14.614	-2.9841	-3.5328	3.3869	-0.2614	3.8058	-0.0214	0.2299	-0.1355	-0.237	-0.0529	0.1202	-0.0672	-0.0087	0.0742	0.113	0.0053	-0.0044	0.0903	-0.0209	0.0308	27.5321	30.3932	4.3645
10	12.6495	-2.585	-2.457	3.7949	-1.8405	3.8368	0.099	0.2363	0.0863	-0.0409	-0.0276	0.2361	-0.0771	-0.1209	-0.0714	0.0759	-0.0031	-0.0036	0.0375	-0.0034	0.0539	12.4213	39.4368	11.4122
11	1.2997	1.1029	-1.543	4.1246	-1.6379	6.4003	0.0161	0.0515	0.1827	0.0075	-0.0095	0.2201	-0.3482	-0.1044	-0.0065	0.0515	-0.0083	-0.0142	0.0611	0.0115	0.0472	29.1791	33.532	14.2362
12	4.2047	-4.4947	4.3526	6.2108	-4.3771	4.6163	0.3264	0.3115	-0.078	-0.3976	-0.2999	0.248	0.3868	0.2929	-0.0266	0.1063	-0.0102	-0.0163	0.0906	0.0112	0.0897	10.4596	29.08	12.0713
13	7.4716	-3.0376	2.028	3.1622	-0.2711	4.3818	0.0117	0.0442	-0.2974	0.0929	-0.0097	-0.0493	0.2593	0.0257	-0.002	0.0477	-0.0054	0.0038	0.0257	0.0068	0.0375	28.819	19.024	19.4979
14	8.5911	-6.5766	-1.9751	5.0521	1.4383	4.2609	-0.5397	-0.9722	-0.5128	0.434	0.7386	0.4449	0.0314	0.0832	-0.199	0.1305	0.0747	0.0997	0.1251	0.0594	0.1897	12.0754	29.0626	27.1964
15	1.2794	-4.1962	5.148	13.9211	-17.1652	21.2262	0.2426	0.228	0.085	-0.795	-0.6157	-0.3375	0.9117	0.6289	0.3731	0.163	0.1312	0.1114	0.238	0.0452	0.2371	39.0623	22.3859	10.3285
16	8.2949	7.3217	-9.4709	15.0173	-11.9358	17.822	0.2065	-0.3578	0.2338	0.5407	0.0083	0.4396	-0.4601	-0.103	-0.2148	0.0535	0.0495	0.0408	0.1147	0.0691	0.2183	1.6828	36.5778	21.0951
17	18.266	0.9849	-9.6156	5.3258	-2.483	19.1525	-0.0545	-0.1023	0.8803	0.5634	0.0317	-0.3432	-0.1315	0.2805	0.0228	0.1112	-0.0312	-0.0935	0.0713	0.0287	0.215	37.748	24.0035	24.1843
18	16.5191	-5.8488	11.8115	11.1352	-7.622	9.7651	0.4105	1.136	-0.6141	0.9564	0.2629	0.9743	-0.055	0.5543	-0.6734	0.39	0.0861	0.3383	0.2169	0.1232	0.5984	2.8976	23.0229	24.7233
19	1.646	-1.5581	1.2494	4.8459	-0.4964	4.6346	-0.0198	-0.009	-0.0606	0.1262	-0.0486	-0.3462	0.2224	-0.0708	0.0684	0.0243	-0.0042	0.0175	0.0681	0.0118	0.1043	35.8092	21.3848	18.5713
20	1.1127	2.2204	-2.5709	7.5797	-4.2178	6.3163	-0.1145	-0.0398	-0.0535	0.2155	0.0136	0.3381	0.3471	0.0259	0.1009	0.1002	0.0564	0.0881	0.1371	0.1141	0.2689	4.2611	28.6203	25.5722

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	20 - 32
8	X-RAY DIFFRACTION	4	B	20 - 32
9	X-RAY DIFFRACTION	5	A	11 - 19
10	X-RAY DIFFRACTION	6	B	11 - 19
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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