PDB-3o9a: Crystal Structure of wild-type HIV-1 Protease in complex with kd14

ID or keywords:

Entry

Database: PDB / ID: 3o9a

Title

Crystal Structure of wild-type HIV-1 Protease in complex with kd14

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 / RNA stem-loop binding / RNA-directed DNA polymerase activity / endonuclease activity / aspartic-type endopeptidase activity / proteolysis / DNA binding
Similarity search - Function

Biological species

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.9 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	3o9a.cif.gz	93.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3o9a.ent.gz	73.6 KB	Display	PDB format
PDBx/mmJSON format	3o9a.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3o9a_validation.pdf.gz	771.6 KB	Display	wwPDB validaton report
Full document	3o9a_full_validation.pdf.gz	773 KB	Display
Data in XML	3o9a_validation.xml.gz	11 KB	Display
Data in CIF	3o9a_validation.cif.gz	14.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o9/3o9a ftp://data.pdbj.org/pub/pdb/validation_reports/o9/3o9a	HTTPS FTP

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Related structure data

Related structure data	3o99C 3o9bC 3o9cC 3o9dC 3o9eC 3o9fC 3o9gC 3o9hC 3o9iC C: citing same article (ref.)
Similar structure data	3bgc-d 3ttp-d 4njt-1 1hpo-d 1ebk-2 2qi0-d 3gi6-d 4jec-d 3b80-d 2q55-d 1bv7-d 4f73-d 1meu-d 2pk5-d 3mxd-d 2r3t-d 1mer-d 5kr0-d 4gzf-d 3o9h-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)	50.745, 57.751, 61.876
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) 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-K14 / (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(1S,2R)-1-benzyl-2-hydroxy-3-{[(4-methoxyphenyl)sulfonyl][(2S)-2-methylbutyl]amino}propyl]carbamate Mass: 576.701 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₉H₄₀N₂O₈S
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 113 / 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: 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: Jun 24, 2008

Radiation

Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.9→50 Å / Num. obs: 14888 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / R_merge(I) obs: 0.088 / Net I/σ(I): 10.2

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.9-1.97	6	0.387	1	99.9
1.97-2.05	6.7	0.269	1	100
2.05-2.14	6.8	0.211	1	100
2.14-2.25	7	0.164	1	100
2.25-2.39	7	0.138	1	100
2.39-2.58	7	0.12	1	100
2.58-2.84	7.1	0.094	1	100
2.84-3.25	7	0.07	1	100
3.25-4.09	7	0.054	1	100
4.09-50	6.7	0.056	1	99.5

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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: 1.9→42.22 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.934 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.782 / SU ML: 0.101 / SU R Cruickshank DPI: 0.1696 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21551	752	5.1 %	RANDOM
R_work	0.17918	-	-	-
obs	0.18106	14095	99.84 %	-

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: 22.212 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.15 Å²	0 Å²	0 Å²
2-	-	0.21 Å²	0 Å²
3-	-	-	0.94 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→42.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1486	0	60	113	1659

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	1600
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1057
X-RAY DIFFRACTION	r_angle_refined_deg	1.273	2.023	2189
X-RAY DIFFRACTION	r_angle_other_deg	0.812	3	2608
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.054	5	202
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.341	24.909	55
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.135	15	258
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.889	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	260
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	1732
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	285
X-RAY DIFFRACTION	r_nbd_refined	0.173	0.2	215
X-RAY DIFFRACTION	r_nbd_other	0.191	0.2	1079
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	737
X-RAY DIFFRACTION	r_nbtor_other	0.084	0.2	871
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.127	0.2	98
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	0.207	0.2	21
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.218	0.2	66
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.122	0.2	11
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	0.52	1.5	1060
X-RAY DIFFRACTION	r_mcbond_other	0.113	1.5	418
X-RAY DIFFRACTION	r_mcangle_it	0.756	2	1618
X-RAY DIFFRACTION	r_scbond_it	1.173	3	652
X-RAY DIFFRACTION	r_scangle_it	1.699	4.5	571
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→1.95 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.283	60	-
R_work	0.225	1012	-
obs	-	-	98.53 %

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	3.1223	-0.9673	-0.622	4.5228	1.0564	2.2499	-0.1144	-0.3362	0.0381	0.2678	0.0851	0.0674	0.0167	0.1362	0.0293	0.0007	0.0401	-0.0006	-0.0075	-0.0005	-0.1156	20.9202	25.6326	29.5955
2	4.6734	-2.68	0.1318	2.7313	-0.1165	3.1338	-0.0959	0.0156	-0.4274	0.1808	0.1442	0.2773	0.2919	0.0714	-0.0482	-0.0149	0.0003	0.0382	-0.0854	0.0273	-0.0343	19.8839	17.4174	23.2482
3	2.8522	1.8022	0.5166	4.2459	-1.1652	0.8097	-0.0339	0.0862	-0.0737	0.1018	-0.0573	-0.1021	-0.0465	-0.0234	0.0913	-0.0158	0.0086	-0.0151	-0.0393	-0.0016	-0.0612	27.7614	28.2959	18.9524
4	5.3658	1.2452	1.3375	3.7484	0.4364	1.292	0.1344	-0.136	-0.0664	-0.0387	-0.0227	0.1026	-0.0595	-0.1096	-0.1117	-0.0088	0.0147	0.0049	-0.0746	0.015	-0.0542	12.5233	26.7546	18.7109
5	12.3449	0.869	-5.2044	7.3675	-0.5646	14.9462	-0.2449	-0.5605	-0.4895	0.2781	-0.2736	-1.242	0.1184	1.0368	0.5185	-0.0578	-0.0251	-0.1007	-0.102	0.1037	0.1846	39.7678	30.3924	23.8352
6	16.9917	-9.1105	1.5876	13.764	-4.799	10.0375	0.2397	-0.3241	-0.7476	-0.1156	0.381	1.3461	-0.1083	-0.9452	-0.6207	-0.0918	0.0006	0.0102	0.0169	0.0609	0.1865	0.942	21.5096	18.2013
7	9.7896	0.0075	1.3617	3.2112	3.9144	5.5112	0.0263	0.1481	0.382	-0.1806	0.1175	-0.1658	-0.1986	0.3968	-0.1438	-0.0398	-0.026	0.0012	-0.0613	0.0853	-0.0409	39.6421	31.3407	10.2111
8	9.2085	-0.9388	-0.2953	7.2758	1.3082	4.2149	0.1602	0.2103	-0.0556	-0.1341	0.0271	0.3476	0.2624	-0.5327	-0.1873	-0.0896	-0.0313	-0.0079	0.0032	0.09	-0.0703	0.3962	34.204	13.2692
9	12.2522	-2.0273	-3.1059	0.5822	0.6196	3.4155	0.0429	0.1222	-0.0536	-0.1128	-0.0542	0.0004	-0.0619	-0.0042	0.0114	-0.0147	0.0114	-0.0028	-0.0574	-0.0067	-0.0606	27.5051	30.7171	4.3009
10	9.0958	-2.8026	-2.2187	3.349	-1.3502	2.2054	0.1792	0.2012	0.1317	-0.0113	-0.0489	0.1559	0.014	0.0279	-0.1303	-0.0023	0.0019	-0.0091	-0.0422	-0.0017	-0.0489	12.7977	39.184	11.7447
11	2.3002	1.4305	-2.6819	4.149	-0.4881	7.5949	0.0107	0.1666	0.2085	0.0446	-0.0356	0.2553	-0.3905	-0.2418	0.0249	-0.0389	-0.0078	-0.0225	-0.0348	0.0181	-0.0444	29.0763	33.2159	14.3355
12	6.1036	-3.8457	3.4518	7.2587	-1.5665	4.6567	0.2753	0.3996	-0.2411	-0.3121	-0.0649	0.2846	0.1472	0.1658	-0.2103	-0.0352	-0.0023	-0.0248	-0.052	0.0141	-0.0486	10.4613	29.2596	12.1776
13	0.4724	-0.5671	-0.0963	3.1463	0.9927	0.9944	-0.0695	0.0903	-0.0222	-0.116	-0.0288	-0.0848	0.0338	0.0131	0.0983	-0.0035	-0.0015	0.0002	-0.0295	0.0098	-0.013	28.6587	19.3189	19.4498
14	6.5891	-3.0424	-3.929	4.3758	-0.9376	4.8914	-0.2142	-0.4385	0.06	0.114	0.3886	0.2443	0.073	0.0255	-0.1744	0.0032	0.0439	0.0265	0.0013	0.0262	-0.0435	11.9144	28.9153	27.2906
15	0.3462	-1.339	3.0223	14.4287	-18.8234	31.8867	0.245	0.1781	-0.608	-1.034	-0.8767	-0.6747	0.756	1.2092	0.6317	-0.1123	0.0724	0.0829	0.023	0.068	0.0603	38.8303	22.9233	10.3041
16	10.112	6.3655	-5.0943	10.5416	-10.8931	15.6411	0.3418	-0.3344	0.603	0.6546	0.152	0.7268	-0.7409	-0.1372	-0.4938	-0.0759	0.0779	0.027	-0.062	0.0539	0.0507	1.649	36.5973	21.1836
17	8.5598	-0.6903	-6.6893	13.1071	2.7954	36.7686	0.1854	-0.2451	0.8055	0.3888	0.0571	-0.3025	-0.2258	0.5945	-0.2426	-0.1028	-0.0464	-0.1079	-0.1307	0.0279	0.0267	37.5972	24.08	24.2212
18	37.422	-22.6896	1.5484	14.0702	0.868	10.4928	-0.3787	0.7132	-0.7964	0.5057	-0.0306	0.4684	0.7866	0.3922	0.4093	0.0104	0.0552	0.0443	0.0207	0.0522	0.0766	2.8572	22.9023	24.5937
19	1.3058	-0.0715	1.7738	2.9674	-3.9907	7.6514	0.0344	-0.0219	-0.0907	0.0386	0.047	-0.1243	-0.2266	0.047	-0.0814	-0.0721	0.0179	0.0218	-0.0335	0.0299	0.0349	35.6957	21.6932	18.3052
20	3.0069	1.8221	-4.8237	4.9387	-5.8906	10.0348	-0.0737	-0.0201	0.0517	-0.2627	0.2794	0.5125	0.1956	0.0874	-0.2057	-0.0351	0.017	0.0079	-0.0635	0.0365	0.0431	4.1086	28.5476	25.5205
21	9.3552	-2.4402	-2.5024	4.6848	0.2811	5.7547	0.0843	-0.0351	0.1744	0.0174	-0.0407	-0.2567	-0.264	-0.0875	-0.0436	-0.0688	0.014	-0.0058	-0.0914	0.0097	-0.1107	19.7465	29.7111	13.947

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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Yorodumi