PDB-2q63: HIV-1 PR mutant in complex with nelfinavir

ID or keywords:

Entry

Database: PDB / ID: 2q63

Title

HIV-1 PR mutant in complex with nelfinavir

Components

PROTEASE RETROPEPSIN

Keywords

HYDROLASE / resistance /

nelfinavir

Function / homology

Function and homology information

RNA stem-loop binding /

host cell /

HIV-1 retropepsin /

retroviral ribonuclease H /

exoribonuclease H /

exoribonuclease H activity / host multivesicular body / DNA integration /

RNA-directed DNA polymerase / viral genome integration into host DNA ...
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

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Rezacova, P. / Kozisek, M. / Saskova, K. / Brynda, J. / Konvalinka, J.

Citation

Journal: J.Mol.Biol. / Year: 2007
Title: Molecular analysis of the HIV-1 resistance development: enzymatic activities, crystal structures, and thermodynamics of nelfinavir-resistant HIV protease mutants
Authors: Kozisek, M. / Bray, J. / Rezacova, P. / Saskova, K. / Brynda, J. / Pokorna, J. / Mammano, F. / Rulisek, L. / Konvalinka, J.

History

Deposition	Jun 4, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 26, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Derived calculations / Version format compliance
Revision 1.2	Oct 20, 2021	Group: Database references / Derived calculations / Category: 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	Aug 30, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2q63.cif.gz	58.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2q63.ent.gz	43.1 KB	Display	PDB format
PDBx/mmJSON format	2q63.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q6/2q63 ftp://data.pdbj.org/pub/pdb/validation_reports/q6/2q63	HTTPS FTP

-
Related structure data

Related structure data	2pymC 2pynC 2q64C 1u8gS 2qak C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1hsg-d 3s85-4 6d0d-d 5con-d 6dh4-d 1qbr-d 3so9-d 6ogp-1 6dh3-d 6dh8-d 1hbv-d 5tyr-d 2bb9-d 4hla-d 1upj-1 1pro-d 2cem-d 3kfp-1 3nuj-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

-
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) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #163 - Jul 2013 HIV Capsid similarity (1)

Deposited unit

A: PROTEASE RETROPEPSIN

B: PROTEASE RETROPEPSIN

hetero molecules

22.1 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)	62.500, 62.500, 82.060
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	A

NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	PRO	PRO	PHE	PHE	2	A	A	1 - 99	1 - 99
2	1	PRO	PRO	PHE	PHE	2	B	B	1 - 99	1 - 99
1	2	1UN	1UN	1UN	1UN	1	A	C	1001
2	2	1UN	1UN	1UN	1UN	1	A	C	1001

NCS ensembles :

ID
1
2

Details

the biological assembly is dimer

#1: Protein	PROTEASE RETROPEPSIN / E.C.3.4.23.16 / HIV-1 PROTEASE Mass: 10762.707 Da / Num. of mol.: 2 / Mutation: D30N, L90M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: type B / Gene: gag-pol / Plasmid: pET like, T7 promotor driven / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03367, HIV-1 retropepsin
#2: Chemical	ChemComp-1UN / 2-[2-HYDROXY-3-(3-HYDROXY-2-METHYL-BENZOYLAMINO)-4-PHENYL SULFANYL-BUTYL]-DECAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID TERT-BUTYLAMIDE / NELFINAVIR MESYLATE AG1343 / Nelfinavir Mass: 567.782 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₂H₄₅N₃O₄S / Comment: medication, antiretroviral, protease inhibitor*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.74 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: reservoir solution: 0.5M (NH4)2SO4, 0.1M MES pH 5.4 or pH 5.5; drops: 2+1ul (protein+reservoir}; protein: 3-5mg/ml 5-fold molar excess of inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 3, 2005 / Details: double mirrors X-ray optical system (Bruker)
Radiation	Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.1→54.15 Å / Num. obs: 9287 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / B_iso Wilson estimate: 38 Å² / R_merge(I) obs: 0.085 / Net I/σ(I): 6.3
Reflection shell	Resolution: 2.1→2.2 Å / R_merge(I) obs: 0.411 / Mean I/σ(I) obs: 1.8 / % possible all: 96.1

-
Processing

Software

Name	Version	Classification
HKL-3000		data collection
MOLREP		phasing
REFMAC	5.3	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1U8G

1u8g

Resolution: 2.2→54.15 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.902 / SU B: 14.65 / SU ML: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.532 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25005	881	9.9 %	RANDOM
R_work	0.1843	-	-	-
obs	0.19074	8003	95.74 %	-

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 mean: 25.116 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.21 Å²	0.11 Å²	0 Å²
2-	-	0.21 Å²	0 Å²
3-	-	-	-0.32 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→54.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1506	0	40	118	1664

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	1641
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.32	2.032	2231
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.406	5	198
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.869	24.737	57
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.934	15	282
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.312	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	265
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1166
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	758
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.316	0.2	1109
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.146	0.2	108
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	0.213	0.2	46
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.232	0.2	9
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	0.499	1.5	1015
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.741	2	1592
X-RAY DIFFRACTION	r_scbond_it	1.255	3	720
X-RAY DIFFRACTION	r_scangle_it	1.843	4.5	638
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	395	tight positional	0.04	0.05
2	2	B	40	tight positional	0.01	0.05
1	1	A	359	medium positional	0.07	0.5
1	1	A	395	tight thermal	0.08	0.5
2	2	B	40	tight thermal	0.04	0.5
1	1	A	359	medium thermal	0.09	2

LS refinement shell

Resolution: 2.2→2.258 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.389	62	-
R_work	0.283	454	-
obs	-	-	76.56 %

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	2.1031	3.0982	-1.7093	4.8829	0.7552	34.9925	0.8684	-0.2168	-0.6088	-0.0441	-0.5868	-0.4522	-2.0511	2.9418	-0.2816	0.1227	-0.1825	-0.0829	0.1461	0.0349	0.0669	4.008	60.055	9.357
2	2.8939	-1.0439	1.3448	8.3914	-6.8246	6.3566	-0.017	-0.0222	0.2471	0.2386	0.0043	0.022	-0.338	-0.0601	0.0128	-0.0647	-0.014	-0.0073	-0.1338	-0.0056	-0.1027	-5.426	65.774	-0.516
3	13.1091	-10.5808	3.9984	31.1602	-10.848	6.4946	0.3368	0.2202	0.7574	-0.9101	0.0316	0.9733	0.3492	-0.4917	-0.3684	-0.0768	-0.0487	-0.037	-0.095	0.028	0.0049	-12.853	60.919	-5.551
4	18.8158	7.0716	15.6811	2.9771	4.6893	36.2432	-0.4394	2.065	-0.2137	-3.4985	1.357	0.9785	2.0028	-1.0363	-0.9175	0.2333	-0.0912	-0.0361	0.2082	0.0057	0.2383	-17.85	59.566	-14.123
5	8.2743	6.9774	1.4251	5.8838	1.2017	0.2454	-1.4013	0.0233	0.628	0.5235	0.9681	1.1734	-0.9824	2.532	0.4332	0.4506	0.131	-0.1284	0.3942	0.1034	0.3693	-21.593	53.008	-0.29
6	28.0818	7.116	-0.7765	10.1811	-0.0257	4.2214	0.0022	0.1476	-0.1987	-0.7818	-0.0575	-0.4309	0.45	-0.1026	0.0553	0.2099	0.0723	0.0845	-0.1263	0.096	-0.0532	-7.182	62.629	-11.692
7	1.9664	0.1133	0.801	5.1659	-3.0063	4.4283	-0.1114	0.0788	0.1693	-0.3796	0.2585	0.2456	0.023	-0.1172	-0.1472	-0.023	-0.0035	-0.0047	-0.0967	-0.0003	-0.0442	-9.445	60.136	-6.118
8	29.5767	-8.3815	-21.6789	53.5434	-5.783	18.6699	0.3327	0.4618	1.168	-1.9015	-0.0432	-0.6835	0.08	1.007	-0.2895	0.097	0.0734	0.0757	-0.0139	0.0659	-0.0693	0.328	56.746	-7.23
9	9.0963	2.2892	-2.9991	4.0161	-1.011	22.6548	-0.2543	0.1237	0.1778	0.2026	-0.9464	-0.9157	0.8807	0.5064	1.2007	0.0304	-0.0373	0.0521	0.0226	-0.0419	0.1773	5.341	51.824	3.392
10	5.6675	1.4587	5.6884	5.4243	3.426	31.0666	1.259	0.1676	0.5187	-0.6331	-0.3236	-0.9397	1.7197	2.851	-0.9355	0.138	0.1308	0.1058	0.1624	-0.0641	0.1132	4.005	48.217	-1.339
11	2.8128	1.2773	-6.5332	9.1453	-10.112	22.2765	-0.0799	-0.0919	-0.0515	-0.4694	-0.4419	-0.26	0.3864	0.4494	0.5218	-0.0423	0.0101	-0.0171	-0.13	-0.0251	-0.0932	-3.644	42.192	5.536
12	1.5266	-0.7585	3.9184	30.3031	-17.0948	17.7253	0.2411	-0.1129	-0.0077	-0.4911	0.22	0.0161	0.728	-0.4415	-0.4611	-0.1529	-0.0109	0.0555	-0.1106	0.0083	-0.0389	-7.472	38.509	12.601
13	7.4168	0.1249	-3.1483	5.404	-3.9509	5.8736	0.1459	0.1847	-0.4776	0.3082	-0.0061	0.616	-0.0603	-0.3069	-0.1398	-0.0559	0.0232	0.0067	-0.1514	0.0112	-0.0424	-10.712	48.868	11.424
14	7.0267	-2.6908	0.3535	22.2654	-10.0186	30.6535	-0.4125	-1.1297	-0.2929	3.4021	0.8892	0.8258	-2.7394	-1.1876	-0.4767	0.1726	0.0656	0.1242	0.347	0.0446	0.1659	-17.938	49.7	20.096
15	8.8896	-3.8803	2.1778	8.7171	-3.6272	1.5536	0.2715	-0.3715	0.1092	0.7085	-0.0214	0.6195	-0.2601	-0.4837	-0.2501	0.2098	0.0461	0.103	0.0735	0.0694	0.0302	-15.262	49.625	18.003
16	8.1279	-3.451	4.3257	5.8664	-4.7613	10.661	-0.0578	-0.3872	-0.6434	0.2131	0.2276	-0.2136	-0.3572	0.1649	-0.1698	0.0373	-0.0877	0.0262	-0.2002	-0.0045	0.0284	-5.893	45.466	16.506
17	0.45	-0.1383	-1.5323	6.4949	1.4881	5.3782	-0.2056	0.0879	-0.0295	0.2521	0.0561	0.2882	-0.1117	-0.0033	0.1494	-0.0518	-0.0445	-0.0554	-0.098	0.035	-0.0877	-6.648	50.192	11.305
18	2.3652	1.5057	-5.4722	10.6847	-4.6932	16.5974	-0.077	-0.0533	-0.1695	-0.3162	-0.5119	-0.8972	0.2182	0.703	0.5888	-0.0473	0.0472	-0.0904	0.1303	-0.0137	0.1022	4.474	54.684	7.998

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 6	1 - 6
2	X-RAY DIFFRACTION	2	A	A	7 - 14	7 - 14
3	X-RAY DIFFRACTION	3	A	A	28 - 36	28 - 36
4	X-RAY DIFFRACTION	4	A	A	37 - 47	37 - 47
5	X-RAY DIFFRACTION	5	A	A	48 - 55	48 - 55
6	X-RAY DIFFRACTION	6	A	A	56 - 69	56 - 69
7	X-RAY DIFFRACTION	7	A	A	70 - 88	70 - 88
8	X-RAY DIFFRACTION	8	A	A	89 - 93	89 - 93
9	X-RAY DIFFRACTION	9	A	A	94 - 99	94 - 99
10	X-RAY DIFFRACTION	10	B	B	1 - 6	1 - 6
11	X-RAY DIFFRACTION	11	B	B	7 - 14	7 - 14
12	X-RAY DIFFRACTION	12	B	B	15 - 23	15 - 23
13	X-RAY DIFFRACTION	13	B	B	24 - 36	24 - 36
14	X-RAY DIFFRACTION	14	B	B	37 - 50	37 - 50
15	X-RAY DIFFRACTION	15	B	B	51 - 64	51 - 64
16	X-RAY DIFFRACTION	16	B	B	65 - 80	65 - 80
17	X-RAY DIFFRACTION	17	B	B	81 - 91	81 - 91
18	X-RAY DIFFRACTION	18	B	B	92 - 99	92 - 99

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi