PDB-3o9e: Crystal Structure of wild-type HIV-1 Protease in complex with af60

ID or keywords:

Entry

Database: PDB / ID: 3o9e

Title

Crystal Structure of wild-type HIV-1 Protease in complex with af60

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

host multivesicular body / 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 / virion membrane / proteolysis / DNA binding / zinc ion binding
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: Chem.Biol. / Year: 2013
Title: Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance.
Authors: Nalam, M.N. / Ali, A. / Reddy, G.S. / Cao, H. / Anjum, S.G. / Altman, M.D. / Yilmaz, N.K. / Tidor, B. / Rana, T.M. / Schiffer, C.A.

History

Deposition	Aug 4, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 10, 2011	Provider: repository / Type: Initial release
Revision 1.1	Nov 27, 2013	Group: Database references
Revision 1.2	Feb 21, 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
Revision 1.3	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3o9e.cif.gz	94.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3o9e.ent.gz	73.8 KB	Display	PDB format
PDBx/mmJSON format	3o9e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3o9e_validation.pdf.gz	794.6 KB	Display	wwPDB validaton report
Full document	3o9e_full_validation.pdf.gz	796.2 KB	Display
Data in XML	3o9e_validation.xml.gz	11.6 KB	Display
Data in CIF	3o9e_validation.cif.gz	16 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o9/3o9e ftp://data.pdbj.org/pub/pdb/validation_reports/o9/3o9e	HTTPS FTP

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Related structure data

Related structure data	3o99C 3o9aC 3o9bC 3o9cC 3o9dC 3o9fC 3o9gC 3o9hC 3o9iC C: citing same article (ref.)
Similar structure data	3sa6-d 3sac-d 2q55-d 4rvx-2 2bpx-d 3qrs-d 6w6t-d 2qnp-d 6c8x-d 1wbk-d 2pwr-d 4cpt-d 4rvi-2 2uxz-d 5jfp-d 2r38-d 1hsg-d 4rvx-1 1npa-d 3o9c-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

22.6 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)	50.713, 57.843, 61.790
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Pol polyprotein Mass: 10815.790 Da / Num. of mol.: 2 / Fragment: HIV-1 protease (UNP residues 1 to 99) / 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: Q90K99
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-A60 / (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(1S,2R)-3-{[(4-aminophenyl)sulfonyl](2-ethylbutyl)amino}-1-benzyl-2-hydroxypropyl]carbamate Mass: 575.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₉H₄₁N₃O₇S
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 148 / 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: 41.28 %
Crystal grow	Temperature: 295 K / Method: hanging drop, vapor diffusion / pH: 6.2 Details: 126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, 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: 0.9 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2008

Radiation

Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9 Å / Relative weight: 1

Reflection

Resolution: 1.5→50 Å / Num. obs: 29740 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / R_merge(I) obs: 0.045 / Χ²: 1.04 / Net I/σ(I): 13.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.5-1.55	5.8	0.271	2907	1.02	1	99.9
1.55-1.62	5.8	0.212	2934	1.009	1	100
1.62-1.69	5.8	0.162	2951	1.017	1	100
1.69-1.78	5.8	0.121	2937	1.042	1	100
1.78-1.89	5.8	0.09	2947	1.036	1	99.9
1.89-2.04	5.7	0.067	2947	1.078	1	99.9
2.04-2.24	5.7	0.057	2991	0.995	1	100
2.24-2.56	5.6	0.057	2983	1.075	1	99.9
2.56-3.23	5.6	0.044	3022	1.089	1	99.8
3.23-50	5.3	0.022	3121	1.038	1	98.1

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Processing

Software

Name	Version	Classification
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
Starting model: PDB entry ?

Resolution: 1.5→39.19 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.955 / WR_factor R_free: 0.2051 / WR_factor R_work: 0.1791 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.894 / SU B: 2.066 / SU ML: 0.043 / SU R Cruickshank DPI: 0.0753 / SU R_free: 0.0769 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1967	1504	5.1 %	RANDOM
R_work	0.167	-	-	-
obs	0.1686	29687	99.74 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 49.49 Å² / B_iso mean: 18.572 Å² / B_iso min: 7.82 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.66 Å²	0 Å²	0 Å²
2-	-	0.18 Å²	0 Å²
3-	-	-	0.49 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→39.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1498	0	64	148	1710

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	1625
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1091
X-RAY DIFFRACTION	r_angle_refined_deg	1.433	2.026	2219
X-RAY DIFFRACTION	r_angle_other_deg	0.838	3	2692
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.177	5	204
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.988	25	56
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.45	15	272
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.764	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	261
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1756
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	291
X-RAY DIFFRACTION	r_nbd_refined	0.182	0.2	235
X-RAY DIFFRACTION	r_nbd_other	0.202	0.2	1110
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	740
X-RAY DIFFRACTION	r_nbtor_other	0.085	0.2	891
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.101	0.2	88
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.158	0.2	13
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.195	0.2	45
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.086	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	0.818	1.5	1067
X-RAY DIFFRACTION	r_mcbond_other	0.179	1.5	420
X-RAY DIFFRACTION	r_mcangle_it	1.056	2	1634
X-RAY DIFFRACTION	r_scbond_it	1.735	3	667
X-RAY DIFFRACTION	r_scangle_it	2.453	4.5	585

LS refinement shell

Resolution: 1.5→1.539 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.227	99	-
R_work	0.171	2082	-
all	-	2181	-
obs	-	-	99.91 %

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	2.413	-1.0612	-0.1563	2.1086	0.1079	1.6254	-0.1863	-0.2802	0.07	0.3284	0.1196	-0.0986	-0.078	0.055	0.0668	0.0201	0.0423	0.0018	0.0122	-0.0042	-0.0875	20.9004	26.1138	29.6836
2	3.0231	-2.4463	0.2196	2.3755	0.1672	2.2998	-0.1292	-0.0889	-0.3189	0.1741	0.1611	0.2464	0.2042	-0.0888	-0.0319	0.0051	0.0011	0.0309	-0.0425	0.0279	-0.0252	19.6726	17.4479	23.2308
3	2.0318	0.5231	0.4824	2.3661	-0.7551	1.1317	-0.0267	0.0067	-0.0214	0.0548	-0.0937	-0.1243	-0.0614	0.0378	0.1203	-0.021	0.0027	-0.0105	-0.0238	0.0084	-0.0335	27.7516	28.3208	18.932
4	2.9218	-1.2492	0.267	3.0818	-0.9547	1.1779	-0.0247	-0.0292	-0.0925	-0.0849	0.0986	0.2129	-0.0423	-0.0758	-0.074	-0.0247	0.008	0.0017	-0.0373	0.0063	-0.0286	12.4074	26.7135	18.6501
5	8.9202	-2.6592	-3.1566	4.2706	0.5216	5.2182	0.0824	-0.3218	-0.2317	0.2293	-0.2948	-0.8126	-0.2033	0.3845	0.2125	-0.0517	-0.0412	-0.0906	-0.0361	0.0881	0.1287	39.6855	30.4246	23.9637
6	21.3524	-10.1006	-2.6388	4.8032	0.9651	3.5082	0.1751	0.2001	-0.9453	-0.1592	-0.0829	0.3141	-0.0001	-0.4458	-0.0922	-0.0525	-0.0239	-0.0106	0.019	0.0237	0.0889	0.8783	21.4539	18.0321
7	3.7308	-0.1482	0.3977	2.4772	2.8812	4.903	0.023	0.1705	0.0353	-0.0453	0.0697	-0.2243	-0.1041	0.4587	-0.0927	-0.0356	-0.0149	0.0044	0.0081	0.0431	-0.0036	39.6316	31.4238	10.2159
8	5.0058	-0.1398	-0.7296	4.5162	2.2434	2.4836	0.0782	0.3126	0.0678	-0.051	-0.0264	0.3589	0.0414	-0.4049	-0.0518	-0.0491	0.0034	0.0036	0.0241	0.0591	-0.0255	0.4532	34.2065	13.2606
9	9.1673	-0.7937	-1.7487	0.8259	0.0103	1.9263	0.0136	0.2298	-0.0853	-0.1072	-0.0116	0.0255	-0.042	0.0281	-0.002	-0.0131	0.0141	0.0031	-0.0269	-0.0057	-0.05	27.5516	30.8485	4.3024
10	8.5642	-2.7158	-0.4396	2.474	-0.9631	0.9419	0.1172	0.0342	0.0436	-0.0282	-0.0062	0.1275	-0.0478	0.0158	-0.111	-0.0127	-0.0034	-0.0022	-0.033	0.0024	-0.0277	12.4941	39.426	11.561
11	1.6369	0.5976	-0.794	2.6966	-0.7247	3.015	-0.0622	0.0374	0.0514	-0.0103	-0.0533	0.0958	-0.1365	0.0374	0.1155	-0.0104	-0.0125	-0.0211	-0.0281	0.0084	-0.0316	29.0582	33.2439	14.3717
12	3.6221	-2.3919	2.9435	3.2366	-2.0973	4.09	0.121	0.1953	0.0006	-0.2222	-0.0516	0.1347	0.2738	0.1375	-0.0693	-0.0139	0.0022	-0.0127	-0.0344	0.0075	-0.0261	10.414	29.265	12.1615
13	1.4643	-1.5981	-0.3285	2.6739	-0.2996	1.0618	-0.0457	-0.0082	-0.121	-0.0377	0.0043	-0.1381	0.0254	-0.0076	0.0414	-0.0161	0.0077	0.0013	-0.0304	0.0052	-0.0119	28.6135	19.3306	19.3859
14	3.7373	-1.3425	-1.8812	2.4829	-1.3145	3.0778	-0.2437	-0.4723	0.0652	0.1806	0.3325	0.1692	-0.0372	-0.0203	-0.0888	-0.0042	0.0515	0.02	0.0242	0.0135	-0.0522	11.8081	28.8555	27.173
15	2.65	0.2634	0.5039	8.5326	-11.6969	21.7861	0.0383	0.109	-0.5819	-0.6019	-0.5735	-0.3443	0.5263	0.9353	0.5353	-0.067	0.064	0.0836	0.002	0.0609	0.0485	38.8305	23.0436	10.3303
16	7.1489	6.6855	-7.3395	9.4356	-7.8334	13.3373	0.3725	-0.2264	0.434	0.4993	0.3152	0.6494	-0.5286	-0.0264	-0.6876	-0.0442	0.08	0.0549	-0.0278	0.0582	0.0488	1.6745	36.572	21.2166
17	11.4745	-0.8403	-2.4788	9.7493	2.3881	14.4392	-0.2063	-0.0076	0.9722	0.4949	-0.0515	-0.2563	-0.0641	0.2509	0.2578	-0.0775	-0.0306	-0.0996	-0.1098	0.0654	0.0667	37.4837	24.1048	24.2576
18	20.659	-8.6722	1.6587	5.8132	3.2623	9.7049	-0.3261	0.5556	-0.1771	0.3049	-0.0516	-0.1148	0.5979	0.552	0.3777	-0.042	0.0495	0.054	0.0157	0.0672	-0.0237	2.7371	22.9129	24.4148
19	1.3553	-1.3101	0.9266	4.0153	-3.904	8.3287	-0.023	0.0483	0.0466	0.024	-0.2195	-0.4003	0.1043	0.381	0.2425	-0.0664	0.0007	0.0059	-0.0292	0.0355	0.0281	36.3524	21.3661	19.3062
20	2.7771	2.9012	-5.2013	5.9898	-5.5996	9.7509	-0.1033	-0.1233	-0.0437	-0.0153	0.0847	0.1939	0.0271	-0.0126	0.0186	-0.0631	0.0336	0.0082	0.0074	0.0501	0.0252	4.0238	28.5069	25.4774

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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Yorodumi