PDB-3o9d: Crystal Structure of wild-type HIV-1 Protease in complex with kd19

ID or keywords:

Entry

Database: PDB / ID: 3o9d

Title

Crystal Structure of wild-type HIV-1 Protease in complex with kd19

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

viral genome integration into host DNA / establishment of integrated proviral latency / telomerase activity / RNA stem-loop binding / endonuclease activity / aspartic-type endopeptidase activity / proteolysis / DNA binding / zinc ion binding
Similarity search - Function

Biological species

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.85 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	Sep 28, 2011	Group: Refinement description
Revision 1.2	Nov 27, 2013	Group: Database references
Revision 1.3	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.4	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 1.5	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3o9d.cif.gz	93 KB	Display	PDBx/mmCIF format
PDB format	pdb3o9d.ent.gz	72.7 KB	Display	PDB format
PDBx/mmJSON format	3o9d.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/o9/3o9d ftp://data.pdbj.org/pub/pdb/validation_reports/o9/3o9d	HTTPS FTP

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Related structure data

Related structure data	3o99C 3o9aC 3o9bC 3o9cC 3o9eC 3o9fC 3o9gC 3o9hC 3o9iC C: citing same article (ref.)
Similar structure data	2qi7-d 1d4k-d 2psv-d 1hpo-d 3hdk-d 2qci-d 1mtb-d 1ec3-d 2i4d-d 6oxp-d 5ah9-d 2nxl-d 3bgc-d 3saa-d 1fg6-d 4mc1-d 4obf-2 4q1y-d 6oxz-d 5ahb-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

22.5 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)	50.708, 57.600, 61.718
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.: 2 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-K19 / (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(1S,2R)-3-{(1,3-benzothiazol-6-ylsulfonyl)[(2S)-2-methylbutyl]amino}-1-benzyl-2-hydroxypropyl]carbamate Mass: 603.750 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₉H₃₇N₃O₇S₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.08 Å³/Da / Density % sol: 40.96 %
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:

ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å

Detector

Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 20, 2009

Radiation

Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.85→50 Å / Num. obs: 15998 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / R_merge(I) obs: 0.06 / Net I/σ(I): 12.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.85-1.88	6.2	0.346	1	97
1.88-1.92	6.8	0.297	1	99.9
1.92-1.95	6.9	0.288	1	99.4
1.95-1.99	6.9	0.247	1	99.6
1.99-2.04	7	0.21	1	100
2.04-2.08	7	0.188	1	99.9
2.08-2.14	6.9	0.155	1	99.9
2.14-2.19	7.1	0.13	1	100
2.19-2.26	7	0.111	1	100
2.26-2.33	7	0.107	1	100
2.33-2.41	7	0.096	1	100
2.41-2.51	7.1	0.088	1	100
2.51-2.63	7.1	0.076	1	100
2.63-2.76	7.1	0.068	1	100
2.76-2.94	7.1	0.059	1	100
2.94-3.16	7.1	0.049	1	100
3.16-3.48	7.1	0.043	1	100
3.48-3.99	7.1	0.036	1	100
3.99-5.02	7	0.033	1	100
5.02-50	6.5	0.04	1	98.8

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
DENZO		data reduction
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry ?

Resolution: 1.85→39.19 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.935 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.059 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1529 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22613	795	5 %	RANDOM
R_work	0.17412	-	-	-
obs	0.17657	15156	99.79 %	-

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 mean: 29.054 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.66 Å²	0 Å²	0 Å²
2-	-	-0.33 Å²	0 Å²
3-	-	-	0.99 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→39.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1480	0	59	94	1633

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	1623
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1067
X-RAY DIFFRACTION	r_angle_refined_deg	1.372	2.021	2223
X-RAY DIFFRACTION	r_angle_other_deg	0.856	3	2641
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.274	5	208
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.621	25.273	55
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.865	15	263
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.598	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	264
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	1783
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	287
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.61	1.5	1020
X-RAY DIFFRACTION	r_mcbond_other	0.154	1.5	424
X-RAY DIFFRACTION	r_mcangle_it	1.078	2	1655
X-RAY DIFFRACTION	r_scbond_it	1.626	3	603
X-RAY DIFFRACTION	r_scangle_it	2.449	4.5	568
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.85→1.898 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.222	58	-
R_work	0.169	1070	-
obs	-	-	98.69 %

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	3.2777	-0.7105	-0.3648	3.0676	0.3904	1.488	-0.1029	-0.3132	-0.0102	0.2612	0.0371	0.1098	-0.0004	0.1333	0.0658	0.0019	0.0299	0.0148	-0.0119	0.0039	-0.1095	20.8687	25.5993	29.5937
2	3.5591	-1.5568	0.2057	1.5107	0.285	3.4229	-0.0378	-0.0066	-0.2518	0.113	0.1471	0.2267	0.1811	-0.0361	-0.1093	-0.026	0.0034	0.0314	-0.0677	0.0216	-0.032	19.7525	17.3655	23.2723
3	2.1783	0.9188	-0.1535	2.4463	-0.9279	0.8314	0.0182	-0.0024	-0.0101	0.0789	-0.0547	-0.0481	-0.0326	0.0113	0.0364	-0.0224	0.0069	-0.0092	-0.0207	0.0043	-0.0452	27.7296	28.183	18.9351
4	4.0438	0.9035	0.8465	2.4425	0.3237	1.6184	0.0201	0.0022	-0.1005	0.0096	0.0627	0.0908	-0.0515	-0.0429	-0.0828	-0.024	0.0076	0.0127	-0.0415	0.0119	-0.0405	12.4812	26.6835	18.6663
5	4.5157	-0.6064	-2.8153	3.8101	-2.6525	7.6072	-0.4313	-0.4224	-0.2236	0.204	-0.0738	-0.8475	0.3446	0.6011	0.5051	-0.0128	-0.0408	-0.0565	-0.0311	0.031	0.108	39.5067	30.2963	23.7259
6	7.2863	-3.4526	1.0544	4.3588	-2.0022	7.8252	0.1433	-0.1752	-0.4367	-0.016	0.1636	0.5089	-0.1866	-0.5646	-0.3069	-0.0796	-0.023	0.0133	-0.0183	0.0135	0.0831	1.5829	21.7895	17.7657
7	4.3766	-0.2716	-0.1413	2.8502	2.8384	3.7436	0.0611	0.1308	0.2294	-0.0032	0.0311	-0.3227	-0.2089	0.289	-0.0922	-0.017	-0.0147	0.0123	0.0033	0.0526	-0.0063	39.5997	31.2173	10.2465
8	5.6872	-0.8937	-0.7002	6.0929	1.7628	2.9503	0.0252	0.1789	-0.0841	-0.0595	0.044	0.3698	0.169	-0.3612	-0.0692	-0.0812	-0.0214	-0.0026	0.0027	0.0676	-0.0395	0.4312	34.1803	13.2657
9	8.0656	-1.1078	-1.6128	0.6665	0.0422	1.9985	0.0287	0.1955	-0.0341	-0.141	-0.0535	-0.0005	-0.0269	0.0174	0.0249	-0.0074	0.0124	0.0018	-0.0281	-0.006	-0.0462	27.5162	30.6129	4.3122
10	7.4396	-2.3307	-1.7625	1.8505	-0.2844	1.0423	0.1005	0.1757	0.0962	-0.0384	-0.0252	0.0636	-0.0564	-0.0109	-0.0752	-0.0022	0.0058	-0.0031	-0.0314	-0.0025	-0.0292	12.7893	39.0964	11.7099
11	0.9329	0.7584	-1.2678	2.1238	-0.366	4.9317	0.0155	0.0721	0.0991	-0.0092	-0.0318	0.1703	-0.214	-0.0627	0.0163	-0.0286	-0.0062	-0.0122	-0.018	0.0113	-0.0147	29.0257	33.107	14.3034
12	2.9844	-2.5392	1.8886	3.6155	-0.9055	1.5331	0.1779	0.2288	-0.1387	-0.1804	-0.0158	0.1797	0.1857	0.0889	-0.1622	-0.0307	-0.0055	-0.0268	-0.0272	0.0139	-0.0218	10.4512	29.1968	12.1723
13	1.1175	-0.3035	-0.9102	1.5096	0.4524	0.7708	-0.0604	0.0534	-0.0963	0.0303	0.0455	-0.0819	0.0108	-0.01	0.0149	-0.0112	0.0002	-0.0057	-0.0034	0.0061	-0.003	28.6084	19.2241	19.4707
14	3.3302	-1.053	-2.663	4.8507	-0.9586	2.8473	-0.0816	-0.3681	-0.1102	0.1463	0.112	0.137	-0.0405	-0.0375	-0.0304	-0.0111	0.0338	0.0286	0.0076	0.0337	-0.031	11.8681	28.8913	27.2525
15	0.9887	-2.3472	1.6105	5.6802	-4.547	7.4791	0.0847	0.0341	-0.1915	-0.3316	-0.2537	-0.3197	0.1988	0.1691	0.169	-0.0454	0.0242	0.0262	0.0123	0.0245	0.022	38.8058	22.8078	10.3172
16	4.3472	1.9411	-1.2374	3.7948	-4.9936	7.1145	0.1081	-0.1763	0.1278	0.0996	0.059	0.154	-0.2356	-0.0507	-0.1671	-0.0442	0.0296	0.0184	-0.0287	0.0228	0.0194	1.6145	36.5992	21.1338
17	2.6058	0.5994	-1.5086	2.6347	0.173	5.6078	-0.0241	-0.0581	0.1643	0.1536	-0.0044	-0.0838	-0.0613	0.1278	0.0286	-0.0278	-0.0061	-0.0286	-0.0216	0.0053	-0.0006	37.5333	23.965	24.2664
18	7.4761	-3.2289	2.2364	4.3027	0.4045	4.1485	0.0429	0.256	-0.1606	0.125	-0.1441	0.1646	0.1432	0.1564	0.1012	-0.0478	0.0144	0.0415	-0.0125	0.0268	-0.001	2.7961	22.9162	24.5648
19	1.8764	-0.6276	1.0911	2.1228	-1.0731	4.539	0.0018	0.0243	-0.0901	-0.0026	-0.0215	-0.2122	0.0118	0.0861	0.0197	-0.0436	0.0023	0.0056	-0.0376	0.0174	-0.0128	35.6584	21.5927	18.325
20	0.3681	0.6035	-1.1428	2.6358	-2.5932	4.7321	-0.0841	-0.0544	0.0084	-0.109	0.1745	0.2901	0.039	-0.0353	-0.0904	-0.0419	0.0313	0.0155	-0.0449	0.0482	0.0198	4.0589	28.5507	25.4777
21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

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	20 - 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	57 - 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
25	X-RAY DIFFRACTION	21	A	200

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