PDB-3sa5: Crystal structure of wild-type HIV-1 protease in complex with AF69

ID or keywords:

Entry

Database: PDB / ID: 3sa5

Title

Crystal structure of wild-type HIV-1 protease in complex with AF69

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: 1.65 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	3sa5.cif.gz	99.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3sa5.ent.gz	77.7 KB	Display	PDB format
PDBx/mmJSON format	3sa5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3sa5_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	3sa5_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3sa5_validation.xml.gz	12 KB	Display
Data in CIF	3sa5_validation.cif.gz	16.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sa/3sa5 ftp://data.pdbj.org/pub/pdb/validation_reports/sa/3sa5	HTTPS FTP

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Related structure data

Related structure data	3sa3C 3sa4C 3sa6C 3sa7C 3sa8C 3sa9C 3saaC 3sabC 3sacC 1f7aS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3bgc-d 1mes-d 1meu-d 1izi-d 6dh4-d 3qbf-d 3ia9-d 3ekv-d 2fle-d 3o9a-d 6dh7-d 6pji-d 3sa6-d 3qrs-d 6dh6-d 5ah6-d 2q55-d 2nxd-d 4q1x-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: Protease

B: Protease

hetero molecules

22.7 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)	50.635, 57.315, 61.373
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-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-A69 / N-{(2S,3R)-4-[(1,3-benzothiazol-6-ylsulfonyl)(3-phenylpropyl)amino]-3-hydroxy-1-phenylbutan-2-yl}-3-hydroxybenzamide Type: Peptide-like / Class: Inhibitor / Mass: 615.762 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₃H₃₃N₃O₅S₂ References: N-{(2S,3R)-4-[(1,3-BENZOTHIAZOL-6-YLSULFONYL)(3-PHENYLPROPYL)AMINO]-3-HYDROXY-1-PHENYLBUTAN-2-YL}-3-HYDROXYBENZAMIDE
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.06 Å³/Da / Density % sol: 40.25 %
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: 1.65→50 Å / Num. obs: 21989 / % possible obs: 99.6 % / Redundancy: 6.7 % / R_merge(I) obs: 0.063 / Χ²: 1.09 / Net I/σ(I): 11.4

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.65-1.71	6.8	0.353	2166	1.089	1	99.9
1.71-1.78	6.8	0.272	2160	1.117	1	99.8
1.78-1.86	6.8	0.208	2170	1.139	1	99.9
1.86-1.96	6.8	0.158	2176	1.177	1	99.9
1.96-2.08	6.9	0.121	2177	1.087	1	99.9
2.08-2.24	6.9	0.102	2183	1.071	1	100
2.24-2.46	6.8	0.09	2210	1.051	1	100
2.46-2.82	6.8	0.076	2213	1.045	1	100
2.82-3.55	6.5	0.051	2224	1.028	1	99.7
3.55-50	6.4	0.039	2310	1.09	1	97.1

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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: 1.65→39.06 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.949 / WR_factor R_free: 0.2112 / WR_factor R_work: 0.184 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8888 / SU B: 3.917 / SU ML: 0.063 / SU R Cruickshank DPI: 0.1064 / SU R_free: 0.0998 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.1 / 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	0.2027	1129	5.1 %	RANDOM
R_work	0.1754	-	-	-
obs	0.1767	21945	99.39 %	-

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: 63.92 Å² / B_iso mean: 23.4418 Å² / B_iso min: 12.65 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.05 Å²	0 Å²	0 Å²
2-	-	0.65 Å²	0 Å²
3-	-	-	0.41 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→39.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1494	0	66	119	1679

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	1697
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1144
X-RAY DIFFRACTION	r_angle_refined_deg	1.277	2.053	2318
X-RAY DIFFRACTION	r_angle_other_deg	0.801	3	2800
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.181	5	208
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.202	24.138	58
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.814	15	275
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.025	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	263
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	1853
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	332
X-RAY DIFFRACTION	r_mcbond_it	0.5	1.5	1020
X-RAY DIFFRACTION	r_mcbond_other	0.133	1.5	424
X-RAY DIFFRACTION	r_mcangle_it	0.891	2	1657
X-RAY DIFFRACTION	r_scbond_it	1.519	3	677
X-RAY DIFFRACTION	r_scangle_it	2.329	4.5	661

LS refinement shell

Resolution: 1.651→1.694 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.226	79	-
R_work	0.194	1494	-
all	-	1573	-
obs	-	-	96.8 %

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	2.3538	-1.5077	0.1862	2.3499	0.0293	3.8096	-0.0528	-0.0178	-0.2473	0.1169	0.0374	0.1674	0.1899	-0.0423	0.0153	0.0617	-0.0068	0.0178	0.0239	0.0233	0.0648	19.9967	17.4881	23.7994
2	3.2725	-0.353	0.0389	2.0875	-0.1131	2.2703	-0.0823	-0.276	0.109	0.2256	0.0448	-0.0481	-0.1311	0.0049	0.0376	0.0975	0.0271	0.0032	0.062	-0.0022	0.0072	21.3347	25.9134	29.64
3	5.5955	1.7056	1.9224	1.8703	0.0576	1.8801	0.0123	0.0986	-0.1615	0.0125	0.1516	-0.0942	-0.0501	0.0378	-0.1639	0.0584	0.008	0.0098	0.0352	0.0126	0.057	14.0533	27.6287	19.3446
4	7.4192	2.1627	1.4933	2.4726	-0.2548	0.5686	-0.0889	0.0393	0.2014	0.0682	-0.0331	-0.0016	-0.0809	0.0253	0.122	0.1328	0.0097	-0.0394	0.0777	-0.0093	0.1263	26.508	27.0095	18.3578
5	12.8314	-7.3334	-2.4926	7.2413	1.0498	3.919	0.332	0.2143	-0.3143	-0.2382	-0.2847	0.7356	-0.0672	-0.4701	-0.0473	0.0306	-0.0084	-0.0202	0.0863	-0.0311	0.2607	1.5103	21.528	18.118
6	3.0824	1.6762	-2.8855	5.7448	-1.2798	5.0082	-0.058	-0.0606	-0.0581	0.2132	-0.1625	-0.7429	-0.1957	0.211	0.2205	0.086	-0.028	-0.0846	0.0624	0.0541	0.1912	39.33	30.9118	23.0893
7	5.3184	-2.2989	-0.6042	6.4433	2.1851	4.634	0.1368	0.3418	-0.0261	-0.0506	-0.096	0.3554	0.1697	-0.4881	-0.0408	0.0272	-0.0049	0.0004	0.1305	0.0612	0.0597	0.3092	33.8995	13.1467
8	9.3028	-1.3961	-2.5807	4.4855	4.7217	9.8154	0.0473	0.193	0.2429	-0.1398	-0.0707	-0.0969	-0.1691	0.3563	0.0234	0.058	-0.0137	0.0019	0.118	0.0893	0.0834	39.2145	30.1409	9.2703
9	6.5865	-2.0109	-2.7251	3.7573	-1.5083	2.903	0.089	0.1908	-0.035	-0.0298	-0.0194	0.1226	0.0268	-0.0745	-0.0696	0.1126	0.0328	-0.0026	0.069	-0.0057	0.0553	12.4052	38.9651	11.2339
10	12.0518	-1.7326	-2.9511	1.6295	-0.8534	5.1234	0.0108	0.1558	-0.2163	-0.1132	-0.087	0.0796	-0.086	0.0254	0.0761	0.0752	0.0024	0.0036	0.0358	-0.0128	0.0218	27.6057	29.8996	4.2673
11	6.6384	-5.9317	5.1291	5.9735	-4.1745	5.2717	0.4458	0.5653	-0.0594	-0.4084	-0.397	0.1448	0.3998	0.3923	-0.0488	0.0714	0.0139	-0.0164	0.0835	0.021	0.0583	10.4322	28.841	12.0951
12	0.332	1.0467	0.1155	3.3624	1.0377	9.2499	0.0409	-0.0071	0.104	-0.0048	0.0085	0.334	-0.6433	0.0296	-0.0494	0.1393	-0.0036	-0.0086	0.0775	0.035	0.0981	29.2473	32.9628	14.1061
13	5.0849	-1.472	-2.5741	5.7491	-2.5657	6.3626	-0.26	-0.3594	-0.2169	0.1653	0.3037	0.366	-0.0276	-0.0095	-0.0437	0.0579	0.0355	0.026	0.0687	0.039	0.057	12.2418	29.0695	27.3414
14	3.6686	-2.948	0.7447	2.5522	-0.0219	2.68	-0.0768	0.0737	-0.0009	0.0503	-0.0179	-0.0196	0.031	-0.0125	0.0947	0.078	-0.0077	-0.0004	0.0773	-0.0062	0.0901	28.863	18.9902	19.5725
15	8.4412	6.2462	-5.6187	10.6334	-7.2846	10.7009	0.2286	0.1179	0.3493	0.4808	0.2141	0.3125	-0.5707	-0.3152	-0.4427	0.0439	0.0368	0.0217	0.0621	0.0451	0.0948	1.6441	36.4227	21.217
16	1.3314	-4.0137	2.8642	13.5966	-13.576	22.5538	0.2186	0.1508	0.0169	-0.5999	-0.4602	-0.1368	0.3963	0.4276	0.2416	0.0365	0.0368	0.0254	0.1305	0.0004	0.135	38.884	22.2533	10.2908
17	14.1808	-10.2884	1.2086	11.2667	0.8196	0.8608	-0.1844	0.4431	-0.3621	0.4945	0.1879	0.2975	0.1522	0.2637	-0.0035	0.127	0.0313	0.0811	0.0905	0.011	0.1554	3.2134	22.9227	24.8053
18	11.1811	-2.2844	-9.4164	4.1952	0.8993	15.6137	0.0536	-0.0206	0.6544	0.373	0.1473	-0.3199	0.0559	0.0989	-0.2009	0.0957	-0.0251	-0.0574	0.0719	0.0115	0.1561	37.7739	23.8592	24.0001
19	1.4307	1.098	-2.6127	4.8379	-2.4865	4.8296	-0.0525	-0.0308	-0.0424	0.0025	0.0108	0.3259	0.0991	0.0562	0.0417	0.0592	0.0374	0.0079	0.0871	0.0541	0.1049	4.1091	28.3557	25.6609
20	2.0367	-0.9946	-0.7611	1.7083	0.2596	1.8575	-0.0671	0.1721	-0.1431	0.0242	-0.126	-0.265	0.1377	0.2695	0.1931	0.0985	-0.0023	0.0118	0.0946	0.0261	0.1342	35.7738	21.3185	18.2678

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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