PDB-3sa9: Crystal structure of Wild-type HIV-1 protease in complex With AF68

ID or keywords:

Entry

Database: PDB / ID: 3sa9

Title

Crystal structure of Wild-type HIV-1 protease in complex With AF68

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 /

Biological species

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 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	3sa9.cif.gz	96 KB	Display	PDBx/mmCIF format
PDB format	pdb3sa9.ent.gz	74.6 KB	Display	PDB format
PDBx/mmJSON format	3sa9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sa/3sa9 ftp://data.pdbj.org/pub/pdb/validation_reports/sa/3sa9	HTTPS FTP

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Related structure data

Related structure data	3sa3C 3sa4C 3sa5C 3sa6C 3sa7C 3sa8C 3saaC 3sabC 3sacC 1f7aS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2pqz-d 6dh4-d 6oy1-d 3qbf-d 6dh3-d 2qi6-d 3bgc-d 2qnp-d 6opx-d 6pji-d 6uwc-d 6opu-d 3qrs-d 2r5q-1 2pwr-d 3o9i-d 6opy-d 6dgz-d 3o9c-d 3sac-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

22.3 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)	50.739, 57.520, 61.483
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
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-A68 / N~2~-acetyl-N-[(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]-L-isoleucinamide Type: Peptide-like / Class: Inhibitor / Mass: 561.733 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₉H₄₃N₃O₆S References: N~2~-ACETYL-N-[(2S,3R)-3-HYDROXY-4-{[(4-METHOXYPHENYL)SULFONYL](2-METHYLPROPYL)AMINO}-1-PHENYLBUTAN-2-YL]-L-ISOLEUCINAMIDE
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.07 Å³/Da / Density % sol: 40.69 %
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-BM-C / Wavelength: 0.979

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 17, 2009

Radiation

Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.7→50 Å / Num. obs: 19391 / % possible obs: 95.5 % / Redundancy: 6.1 % / R_merge(I) obs: 0.07 / Χ²: 1.023 / Net I/σ(I): 11.2

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.7-1.76	6.2	0.316	1895	1.027	1	95.9
1.76-1.83	6.2	0.238	1913	0.997	1	96.3
1.83-1.91	6.2	0.174	1939	1.025	1	96.4
1.91-2.02	6.1	0.129	1933	1.092	1	97.1
2.02-2.14	6.2	0.102	1947	0.991	1	96.9
2.14-2.31	6.1	0.085	1941	0.971	1	97.2
2.31-2.54	6.1	0.075	1983	1.033	1	97.4
2.54-2.91	6.1	0.064	1967	1.039	1	96.6
2.91-3.66	5.9	0.054	1961	1.081	1	94.6
3.66-50	5.9	0.053	1912	0.977	1	87.6

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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: 1.7→42 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.941 / WR_factor R_free: 0.2149 / WR_factor R_work: 0.1764 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8736 / SU B: 4.31 / SU ML: 0.07 / SU R Cruickshank DPI: 0.1171 / SU R_free: 0.1146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.115 / 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	0.2139	990	5.1 %	RANDOM
R_work	0.1735	-	-	-
obs	0.1755	19310	95.21 %	-

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: 54.91 Å² / B_iso mean: 20.3054 Å² / B_iso min: 8.71 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.67 Å²	0 Å²	0 Å²
2-	-	0.58 Å²	0 Å²
3-	-	-	1.09 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1498	0	48	118	1664

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	1607
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1077
X-RAY DIFFRACTION	r_angle_refined_deg	1.223	2.016	2193
X-RAY DIFFRACTION	r_angle_other_deg	0.795	3	2659
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.268	5	204
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.193	24.815	54
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.258	15	271
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.709	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	262
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	1753
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	289
X-RAY DIFFRACTION	r_mcbond_it	0.482	1.5	1005
X-RAY DIFFRACTION	r_mcbond_other	0.136	1.5	420
X-RAY DIFFRACTION	r_mcangle_it	0.894	2	1636
X-RAY DIFFRACTION	r_scbond_it	1.596	3	602
X-RAY DIFFRACTION	r_scangle_it	2.612	4.5	557

LS refinement shell

Resolution: 1.703→1.747 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.198	75	-
R_work	0.19	1294	-
all	-	1369	-
obs	-	-	92.94 %

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	2.3537	-0.5311	-0.0471	2.3468	-0.2911	1.8917	-0.0526	-0.1793	0.0569	0.206	0.0347	-0.0095	-0.0987	-0.0049	0.0179	0.0768	0.0278	0.0062	0.0539	-0.0079	0.0043	21.1455	25.8898	29.4442
2	1.0704	-0.9094	-0.1994	2.0213	-0.2778	2.4969	-0.0542	-0.0177	-0.1816	0.0919	0.0667	0.1025	0.1603	-0.0511	-0.0126	0.0544	-0.0033	0.0142	0.0293	0.0026	0.0546	19.7674	17.1411	23.0911
3	4.3366	2.0654	0.6739	2.6829	-0.5687	1.6963	-0.0417	0.0442	0.0339	-0.0087	-0.077	0.0426	-0.1375	-0.0259	0.1187	0.0366	0.0147	-0.0096	0.0146	-0.0089	0.0165	26.4649	27.2059	18.2083
4	3.8354	0.5985	1.4104	2.1143	0.2121	1.6338	0.0072	-0.0209	-0.066	-0.0723	0.1176	0.014	-0.0352	-0.0763	-0.1248	0.0399	0.0007	0.0037	0.0171	0.0131	0.0154	13.8634	27.5316	19.2707
5	2.7679	2.5986	0.4739	4.3865	-1.8999	2.9312	-0.0808	-0.0334	-0.2644	0.1076	-0.272	-0.623	-0.1863	0.2796	0.3528	0.0815	-0.0217	-0.0775	0.0692	0.0361	0.1751	39.3832	30.9323	23.2366
6	7.0352	1.395	-1.6742	0.8819	-0.1429	0.4819	0.0869	0.2823	-0.112	-0.1129	-0.1647	0.502	-0.0978	-0.1896	0.0777	0.1051	0.0721	-0.0642	0.2772	0.019	0.6101	1.4931	21.4393	17.6042
7	6.4663	-0.8906	-0.5774	4.3831	3.3015	6.4665	0.0515	0.1829	0.0904	-0.1234	-0.0184	-0.0522	-0.1198	0.2321	-0.0332	0.0047	-0.0065	-0.0043	0.0601	0.0431	0.0422	39.4503	30.2726	9.3012
8	6.9077	0.3941	-0.6951	3.3218	1.6745	3.5203	0.1591	0.2646	0.0447	0.0089	-0.1301	0.2564	0.092	-0.2946	-0.0291	0.0609	-0.0007	-0.0114	0.0966	0.0345	0.0459	0.3302	33.828	13.0351
9	7.9111	-1.6146	-1.8812	1.9065	-0.0811	4.1335	-0.0558	0.111	-0.054	-0.0553	-0.0032	0.0459	-0.0703	0.0123	0.059	0.0599	0.009	0.0035	0.0174	-0.0019	0.0039	27.5055	30.151	4.3301
10	7.2669	-0.8354	-1.4798	2.1783	-1.666	1.9335	0.0409	0.0575	0.0062	-0.0841	0.0174	0.0927	0.0492	-0.0256	-0.0583	0.0672	0.0003	-0.0048	0.0148	0.0036	0.049	12.3224	39.2484	11.0859
11	0.8194	1.1881	-1.3575	2.7854	-0.1943	5.2125	0.0681	0.0179	0.1076	-0.052	0.038	0.1985	-0.3808	0.0043	-0.1062	0.0477	-0.0112	-0.0089	0.0322	0.0238	0.0476	29.3162	33.1117	14.1716
12	3.2386	-2.2929	1.3838	3.2281	-1.0018	0.5917	0.1498	0.2289	-0.075	-0.2015	-0.1114	0.1402	0.0683	0.0947	-0.0384	0.0521	0.0089	-0.0101	0.0641	0.022	0.0458	10.447	29.0445	11.9811
13	1.6661	-0.8178	0.4636	2.3559	-0.9898	1.7495	-0.0349	-0.0335	-0.0686	0.0568	-0.0258	-0.0485	0.0552	0.0459	0.0607	0.0235	0.0094	-0.0067	0.0123	-0.0017	0.0155	28.7967	19.1986	19.3147
14	4.569	-2.3906	-1.9122	2.4143	-0.4397	2.6357	-0.1749	-0.3752	-0.1709	0.1665	0.2487	0.2271	-0.029	0.0443	-0.0739	0.0574	0.0357	0.0209	0.0915	0.0148	0.054	12.1349	29.0231	27.284
15	1.4874	-3.2699	2.5982	7.5306	-7.4357	13.4014	0.1166	0.1435	-0.0416	-0.2465	-0.323	0.01	0.1056	0.228	0.2064	0.0408	0.0257	0.0349	0.0921	0.0156	0.1293	38.9324	22.6777	10.0781
16	5.0062	2.9471	-4.189	10.0951	-6.6036	7.332	0.0857	-0.0892	0.2913	0.5122	0.2002	0.35	-0.5872	-0.1348	-0.2859	0.0736	0.0288	0.0129	0.0334	0.0378	0.1007	1.7011	36.5878	21.2042
17	8.7455	-1.2983	-4.5907	5.5472	0.7335	7.1466	-0.0129	0.0599	0.3644	0.1942	0.1093	-0.2457	-0.018	0.1128	-0.0964	0.0503	-0.0178	-0.0595	0.031	0.0183	0.0906	37.7986	23.8768	23.9627
18	15.522	-13.3646	0.675	26.0614	6.2622	3.2539	0.0522	0.5864	-0.3922	0.2223	0.0891	0.0215	0.1518	0.3277	-0.1413	0.1042	0.0747	0.0767	0.1455	0.0533	0.1025	3.106	23.0146	24.7024
19	1.9075	-1.0201	0.6556	2.0383	0.6144	3.0956	-0.0569	0.0992	-0.0367	0.0109	-0.0602	-0.2146	0.194	0.1193	0.117	0.04	-0.004	0.0266	0.0327	0.0289	0.0872	35.8144	21.5112	18.0602
20	0.7394	0.9178	-1.0914	1.413	-1.2547	1.6733	-0.1125	0.0023	0.0627	-0.1431	0.1161	0.2764	0.2314	0.054	-0.0036	0.1032	0.0405	0.0063	0.0567	0.0783	0.1507	4.3111	28.5443	25.573

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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