PDB-3lzv: Structure of Nelfinavir-resistant HIV-1 protease (D30N/N88D) in c...

ID or keywords:

Entry

Database: PDB / ID: 3lzv

Title

Structure of Nelfinavir-resistant HIV-1 protease (D30N/N88D) in complex with Darunavir.

Components

HIV-1 Protease

Keywords

HYDROLASE / HIV-1 protease / resistance

Function / homology

Function and homology information

HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...
Similarity search - Function

Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...
Similarity search - Domain/homology

Biological species

HIV-1 M:B_ARV2/SF2 (virus)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Schiffer, C.A. / Kolli, M.

Citation

Journal: J.Virol. / Year: 2010
Title: The Effect of Clade-Specific Sequence Polymorphisms on HIV-1 Protease Activity and Inhibitor Resistance Pathways.
Authors: Bandaranayake, R.M. / Kolli, M. / King, N.M. / Nalivaika, E.A. / Heroux, A. / Kakizawa, J. / Sugiura, W. / Schiffer, C.A.

History

Deposition	Mar 1, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 11, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
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	Oct 13, 2021	Group: Database references / Derived calculations / Structure summary Category: chem_comp / database_2 ...chem_comp / database_2 / struct_ref_seq_dif / struct_site Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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 1.4	Sep 6, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3lzv.cif.gz	56.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3lzv.ent.gz	41.4 KB	Display	PDB format
PDBx/mmJSON format	3lzv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3lzv_validation.pdf.gz	814.9 KB	Display	wwPDB validaton report
Full document	3lzv_full_validation.pdf.gz	817.3 KB	Display
Data in XML	3lzv_validation.xml.gz	10.7 KB	Display
Data in CIF	3lzv_validation.cif.gz	13.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lz/3lzv ftp://data.pdbj.org/pub/pdb/validation_reports/lz/3lzv	HTTPS FTP

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Related structure data

Related structure data	3lzsC 3lzuC 1f7aS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6oxo-d 6p9b-d 5kr0-d 3bgc-d 4rvi-2 6dh7-d 3o9b-d 6uwc-d 1d4j-d 4njt-1 2uxz-d 3mxe-d 2bpx-d 5kr2-3 6oxp-d 1meu-d 1ebz-d 4rvx-1 1ec3-d 1qbs-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 (2) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #163 - Jul 2013 HIV Capsid similarity (1)

Deposited unit

A: HIV-1 Protease

B: HIV-1 Protease

hetero molecules

22.8 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)	50.858, 57.703, 61.614
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	HIV-1 Protease / Protease Mass: 10801.762 Da / Num. of mol.: 2 / Mutation: Q7K, D30N, N88D Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Strain: SF2 / Gene: gag-pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): Tap106 / References: UniProt: P03369, HIV-1 retropepsin
#2: Chemical	ChemComp-017 / (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE / Darunavir / TMC114 / UIC-94017 Mass: 547.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₇H₃₇N₃O₇S / Comment: medication, antiretroviral*YM
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 57 / 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: 41.22 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 126mM Sodium Phosphate pH 6.2; 63mM sodium citrate; 24-29% ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

Diffraction	Mean temperature: 93 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 21, 2005 / Details: Osmic mirrors
Radiation	Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.15→25 Å / Num. obs: 10326 / Observed criterion σ(I): 9.6 / Redundancy: 10.5 % / R_merge(I) obs: 0.067 / R_sym value: 0.095 / Net I/σ(I): 9.6
Reflection shell	Resolution: 2.15→2.23 Å / Redundancy: 10.4 % / R_merge(I) obs: 0.474 / Num. unique all: 997 / R_sym value: 0.537

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing
REFMAC	5.2.0005	refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F7A

1f7a

Resolution: 2.15→23.97 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.939 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.802 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.276 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.236	496	4.8 %	RANDOM
R_work	0.181	-	-	-
obs	0.184	10293	99.22 %	-

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: 100.83 Å² / B_iso mean: 35.539 Å² / B_iso min: 20.82 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.18 Å²	0 Å²	0 Å²
2-	-	0.92 Å²	0 Å²
3-	-	-	1.27 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→23.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1485	0	75	57	1617

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	1583
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1521
X-RAY DIFFRACTION	r_angle_refined_deg	1.785	2.028	2159
X-RAY DIFFRACTION	r_angle_other_deg	0.831	3	3524
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	10.283	5	196
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	45.04	24.717	53
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.992	15	253
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.855	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	256
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1696
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	283
X-RAY DIFFRACTION	r_nbd_refined	0.192	0.2	229
X-RAY DIFFRACTION	r_nbd_other	0.189	0.2	1488
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	699
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	983
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.17	0.2	61
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.108	0.2	10
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.173	0.2	51
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.123	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	1.078	1.5	1259
X-RAY DIFFRACTION	r_mcbond_other	0.212	1.5	412
X-RAY DIFFRACTION	r_mcangle_it	1.295	2	1590
X-RAY DIFFRACTION	r_scbond_it	1.781	3	669
X-RAY DIFFRACTION	r_scangle_it	2.609	4.5	569

LS refinement shell

Resolution: 2.15→2.202 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.302	25	-
R_work	0.217	699	-
all	-	724	-
obs	-	-	95.39 %

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	3.9824	2.3194	3.7483	2.1164	0.9099	5.6449	-0.0992	0.0885	0.12	-0.1465	0.0663	-0.0409	-0.1655	-0.0723	0.0329	0.0274	-0.0385	-0.0188	-0.0079	0.0269	-0.0587	20.458	8.8759	2.3267
2	19.1476	-3.6095	-0.951	1.6788	3.978	14.5009	-0.3873	0.7886	-0.9791	-0.3355	0.6752	0.0582	0.5165	0.2723	-0.2879	0.0445	-0.0385	0.0063	-0.0613	-0.0169	-0.0267	21.2657	-3.9377	2.748
3	15.5083	7.9385	0.4603	22.6128	-3.8508	0.9139	0.3958	-0.2588	-0.3443	0.5869	-0.0821	-0.0472	-0.394	0.2826	-0.3137	0.041	-0.0093	0.043	-0.0087	-0.0486	-0.0537	19.2348	12.3144	14.8058
4	2.3197	-0.8064	0.177	4.9043	-0.1329	0.0146	0.0206	-0.0004	-0.0028	-0.1775	0.0086	0.013	-0.2631	0.1228	-0.0292	0.0426	-0.0033	0.0154	0.0148	0.0044	-0.0383	25.9864	2.2276	12.8984
5	10.2378	0.9361	0.9082	3.7475	6.8083	12.4319	0.0826	0.0783	0.0375	0.1244	0.1167	0.1789	0.1315	0.3334	-0.1994	-0.0249	-0.0026	-0.0436	-0.0927	0.0666	0.0143	39.671	-2.1054	20.4852
6	5.8902	1.4804	-0.8046	0.3721	-0.2022	0.1099	0.0474	-0.04	0.242	-0.0331	0.0101	-0.0627	0.0901	0.0298	-0.0575	0.0213	-0.0071	-0.0038	-0.0314	-0.0112	0.025	14.382	0.9814	11.3296
7	7.7517	2.0158	0.4996	14.1162	2.9381	5.5339	0.0023	0.0802	-0.0654	0.1094	-0.02	0.388	0.0372	-0.1579	0.0176	-0.1232	-0.0055	0.011	0.0252	0.0468	-0.0511	0.7136	-5.7134	16.8962
8	17.6986	2.0786	5.4246	1.5668	4.4119	12.4357	-0.1917	-0.3252	0.3495	-0.0272	0.1013	0.1472	-0.0092	0.1992	0.0904	0.0289	-0.0054	0.0034	-0.0757	0.012	-0.0437	27.9406	-0.984	27.4481
9	16.9548	6.3387	2.1612	8.7563	-1.8408	1.374	0.3992	0.0149	0.1745	-0.045	-0.0414	0.2127	-0.0186	0.2437	-0.3578	-0.0023	0.0282	-0.0391	0.0256	-0.0355	-0.0751	12.8914	-11.0274	18.8053
10	8.8981	3.4478	3.4322	10.1193	-15.2625	32.6684	0.4325	-0.2124	0.4543	0.5013	-1.5027	-0.5454	-0.6502	0.972	1.0703	-0.0737	0.0314	0.0087	-0.0046	0.044	-0.0495	38.8957	3.5389	21.4441
11	28.7983	-3.5431	19.7233	10.6495	-7.5211	34.5353	-0.1256	0.1449	-0.7645	-0.4854	0.3746	-0.3383	0.1769	0.0915	-0.249	-0.071	0.0451	0.1022	-0.0959	-0.0404	-0.0271	37.1449	4.7886	6.7122
12	1.0661	-0.3367	1.4314	7.2922	-8.0748	10.8135	0.0512	0.0619	0.3488	0.072	-0.261	-0.1454	0.3651	0.7952	0.2098	-0.0443	0.0104	-0.0034	-0.0165	0.0374	0.0237	36.4352	7.3374	12.8974
13	10.2324	-5.973	4.9691	12.6158	-1.2566	2.7092	0.1802	-0.3502	-0.034	-0.9936	0.0701	0.4467	0.0633	-0.3306	-0.2504	0.0234	-0.0513	-0.0471	0.0089	0.0498	0.0378	1.3535	-7.3899	12.2134
14	19.2919	19.8337	-6.5344	31.3421	-2.4309	11.5173	0.2392	-0.3742	1.1917	0.1373	-0.5287	1.1386	-0.037	0.4514	0.2895	-0.0452	-0.0057	-0.1158	-0.0935	0.0031	0.0601	3.1659	5.991	6.5096
15	6.7982	-2.0884	7.6412	9.8805	-8.2738	12.3902	0.0813	-0.02	-0.0823	-0.2644	0.0025	0.4175	0.2827	0.157	-0.0838	-0.0344	0.0344	0.0969	-0.0389	0.038	-0.0104	4.012	-0.6198	5.9528
16	0.4944	-1.8543	0.1172	6.9565	-0.414	0.3888	-0.0863	0.0488	-0.143	-0.2856	-0.2356	0.3238	0.1058	0.0947	0.3219	-0.0013	-0.0073	-0.0043	-0.0022	0.008	0.0187	29.3743	-3.7811	16.1447
17	10.3015	2.1114	-2.9605	3.6416	-0.4034	7.3194	0.3271	-0.337	0.1522	0.2465	-0.0756	0.1899	-0.4399	0.4203	-0.2515	0.0073	-0.0182	0.0051	-0.0537	0.0094	-0.0431	10.4699	-0.1032	18.1952
18	4.067	2.2735	1.573	5.2308	-2.5901	3.6483	-0.0953	0.0577	0.184	0.1703	0.0594	-0.2992	0.0845	-0.1937	0.0359	0.023	-0.0065	0.0197	0.0105	-0.0244	-0.032	28.9079	9.3735	11.2459
19	4.4975	2.9192	2.2667	8.624	-3.8157	5.2962	-0.2408	0.1976	0.2673	0.1002	0.3062	0.3896	-0.2044	0.1837	-0.0655	0.04	-0.0407	-0.013	-0.0034	0.0039	-0.0318	11.7775	0.4273	3.9689
20	2.887	1.2681	3.4737	5.2757	5.4461	7.4367	0.3376	-0.1722	0.0749	0.3701	-0.3046	-0.229	0.5006	-0.3724	-0.033	0.0266	-0.0142	-0.0085	0.0181	0.027	-0.033	19.8198	-0.8178	17.0114

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	B	1 - 5
4	X-RAY DIFFRACTION	1	B	94 - 99
5	X-RAY DIFFRACTION	2	A	6 - 10
6	X-RAY DIFFRACTION	3	B	6 - 10
7	X-RAY DIFFRACTION	4	A	22 - 32
8	X-RAY DIFFRACTION	5	A	33 - 43
9	X-RAY DIFFRACTION	6	B	22 - 32
10	X-RAY DIFFRACTION	7	B	33 - 43
11	X-RAY DIFFRACTION	8	A	44 - 49
12	X-RAY DIFFRACTION	8	A	52 - 56
13	X-RAY DIFFRACTION	9	B	44 - 49
14	X-RAY DIFFRACTION	9	B	52 - 56
15	X-RAY DIFFRACTION	10	A	57 - 62
16	X-RAY DIFFRACTION	11	A	63 - 68
17	X-RAY DIFFRACTION	12	A	69 - 76
18	X-RAY DIFFRACTION	13	B	57 - 62
19	X-RAY DIFFRACTION	14	B	63 - 68
20	X-RAY DIFFRACTION	15	B	69 - 76
21	X-RAY DIFFRACTION	16	A	77 - 85
22	X-RAY DIFFRACTION	17	B	77 - 85
23	X-RAY DIFFRACTION	18	A	86 - 93
24	X-RAY DIFFRACTION	19	B	86 - 93
25	X-RAY DIFFRACTION	20	A	200

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