PDB-3o9f: Crystal Structure of wild-type HIV-1 Protease in complex with kd27

ID or keywords:

Entry

Database: PDB / ID: 3o9f

Title

Crystal Structure of wild-type HIV-1 Protease in complex with kd27

Components

Protease

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

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: 1.7 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 23, 2011	Group: Structure summary
Revision 1.3	May 16, 2012	Group: Refinement description
Revision 1.4	Nov 27, 2013	Group: Database references
Revision 1.5	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.6	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 1.7	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3o9f.cif.gz	95.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3o9f.ent.gz	75.4 KB	Display	PDB format
PDBx/mmJSON format	3o9f.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o9/3o9f ftp://data.pdbj.org/pub/pdb/validation_reports/o9/3o9f	HTTPS FTP

-
Related structure data

Related structure data	3o99C 3o9aC 3o9bC 3o9cC 3o9dC 3o9eC 3o9gC 3o9hC 3o9iC C: citing same article (ref.)
Similar structure data	6oxr-d 1g2k-d 1a94-2 3sa3-d 4u7v-d 3o9g-d 6oxt-d 4djp-d 6oxx-d 1mer-d 1mrw-d 3nu6-d 4dqc-d 2qi1-d 3lzs-d 4tvh-d 5upz-d 4mc6-d 2qhy-d 1met-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) #163 - Jul 2013 HIV Capsid similarity (1)

Deposited unit

A: Protease

B: Protease

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)	50.773, 57.934, 61.794
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Protease / 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, UniProt: P03369*PLUS
#2: Chemical	ChemComp-K2D / (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(1S,2R)-1-benzyl-3-{(2-ethylbutyl)[(4-methoxyphenyl)sulfonyl]amino}-2-hydroxypropyl]carbamate Mass: 590.728 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₀H₄₂N₂O₈S
#3: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.1 Å³/Da / Density % sol: 41.45 %
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

-
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: Apr 18, 2009

Radiation

Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.7→50 Å / Num. obs: 20045 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / R_merge(I) obs: 0.053 / Net I/σ(I): 14.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.7-1.76	3.8	0.371	1	79.7
1.76-1.83	6.2	0.3	1	96.5
1.83-1.91	7	0.204	1	97.3
1.91-2.02	7	0.139	1	97.7
2.02-2.14	7	0.101	1	98.2
2.14-2.31	7	0.087	1	99
2.31-2.54	7	0.07	1	99
2.54-2.91	7	0.051	1	99.6
2.91-3.66	7	0.034	1	99.9
3.66-50	6.6	0.025	1	99.1

-
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: 1.7→39.22 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.943 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.375 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1135 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20364	1018	5.1 %	RANDOM
R_work	0.16853	-	-	-
obs	0.17028	18989	96.71 %	-

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: 26.563 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.63 Å²	0 Å²	0 Å²
2-	-	0.2 Å²	0 Å²
3-	-	-	0.43 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→39.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1494	0	58	137	1689

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	1667
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1111
X-RAY DIFFRACTION	r_angle_refined_deg	1.377	2.019	2280
X-RAY DIFFRACTION	r_angle_other_deg	0.824	3	2749
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.331	5	214
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.711	25.254	59
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.769	15	276
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.48	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	268
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	1844
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	297
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	0.527	1.5	1041
X-RAY DIFFRACTION	r_mcbond_other	0.152	1.5	430
X-RAY DIFFRACTION	r_mcangle_it	0.921	2	1694
X-RAY DIFFRACTION	r_scbond_it	1.538	3	626
X-RAY DIFFRACTION	r_scangle_it	2.37	4.5	586
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.699→1.743 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.39	60	-
R_work	0.288	1077	-
obs	-	-	76.77 %

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	3.2052	-1.5334	0.3936	3.97	-0.36	1.8442	-0.1939	-0.3494	0.0646	0.2906	0.1309	-0.0961	-0.0634	0.0944	0.063	0.0983	0.0383	0.013	0.0841	0.0001	0.0056	20.8431	25.9584	29.5455
2	3.1151	-1.8831	0.1259	1.8479	0.1548	2.2951	-0.1117	-0.0506	-0.3147	0.1501	0.1299	0.2603	0.1761	-0.0676	-0.0182	0.0952	0.005	0.0301	0.0425	0.0241	0.0626	19.5859	17.2854	22.954
3	2.5903	0.6397	1.1171	1.9511	-0.6618	0.958	-0.0423	0.0711	0.0516	0.0485	-0.0323	-0.0607	-0.0581	0.0596	0.0746	0.0694	0.0025	-0.0051	0.0592	0.0011	0.0503	27.7654	28.2567	18.5718
4	3.8546	0.9764	1.1854	3.7339	-0.6158	1.1011	-0.0246	0.0081	-0.0681	-0.0693	0.1031	0.1959	-0.0715	-0.0297	-0.0785	0.0537	0.0127	0.0059	0.0429	0.0095	0.0433	12.4626	26.8992	18.6044
5	0.3458	-2.1524	0.4184	4.3178	1.3284	4.8186	-0.0816	-0.0768	0.1694	0.1344	0.1407	-0.4693	0.0482	0.4166	-0.0591	0.1043	-0.016	-0.0577	0.1695	0.064	0.2537	39.7609	30.4635	24.2455
6	17.246	-4.7231	-4.1347	1.7925	1.5116	0.6899	0.1146	0.2066	-0.381	-0.0186	-0.1515	0.0875	-0.0009	-0.1011	0.0369	0.0233	-0.0181	0.0018	0.0949	0.0042	0.1543	0.7721	21.6366	18.1127
7	5.7731	-0.3069	0.4743	2.6605	2.2975	3.5822	0.0482	0.1803	0.1227	-0.0306	0.1154	-0.3266	-0.0291	0.3316	-0.1635	0.0511	-0.0092	-0.0005	0.0701	0.04	0.0867	39.4574	31.691	10.2631
8	6.2256	-1.7513	-1.7276	6.6362	3.0884	3.8742	0.1125	0.1813	0.0793	-0.121	-0.0739	0.2859	0.0631	-0.4409	-0.0386	0.0309	0.0064	-0.0046	0.1223	0.0695	0.0691	0.3214	34.4501	13.2691
9	8.6424	-1.3001	-1.5567	0.2757	-0.1152	2.8083	-0.011	0.2756	-0.1229	-0.0734	-0.0341	0.0239	-0.0051	0.0711	0.0451	0.1086	-0.0008	0.001	0.0635	0.0014	0.0535	27.4834	31.0056	4.4255
10	4.9176	-1.2784	-1.6264	2.7061	-1.2099	1.5046	0.1195	0.0698	0.1778	0.0271	0.0557	0.1574	-0.0702	-0.0566	-0.1752	0.0728	0.0103	-0.0065	0.0524	0.0027	0.0678	12.5238	39.539	11.5727
11	0.7108	1.0663	-0.7559	1.8268	-0.4711	2.8296	-0.0595	0.0212	0.0631	-0.0266	-0.0615	0.0871	-0.176	-0.023	0.121	0.1179	-0.0186	-0.0309	0.0972	0.0238	0.093	28.9898	33.5827	14.5375
12	4.6607	-2.7443	3.3822	5.2385	-3.8179	3.3426	0.1278	0.2618	-0.0316	-0.2496	-0.0532	0.1143	0.193	0.115	-0.0746	0.055	0.0004	-0.0131	0.0655	0.0058	0.0402	10.4646	29.3197	12.1486
13	2.6015	0.4161	0.6512	3.1722	-1.6232	0.9924	-0.0604	0.0422	0.0015	-0.0384	0.0168	-0.0641	0.0192	0.0127	0.0436	0.0772	0.0078	-0.0007	0.0686	-0.0024	0.0656	28.669	19.2619	19.3734
14	2.4658	-1.7138	-1.6398	1.8926	-0.2487	3.5537	-0.1349	-0.2643	-0.0204	0.0943	0.1902	0.1262	-0.0583	-0.0365	-0.0553	0.0884	0.0656	0.0044	0.143	-0.0099	0.0839	11.8148	28.8312	27.2568
15	0.6281	1.2223	1.3708	9.9318	-11.7128	20.8602	-0.0338	-0.0387	-0.0495	-0.5708	-0.6829	-0.3914	0.5208	0.822	0.7167	0.0519	0.0722	0.054	0.1408	0.044	0.1876	38.7835	22.8837	10.3825
16	8.6919	5.0407	-8.849	8.1173	-5.7371	11.6743	0.4356	-0.3397	0.4075	0.3615	0.066	0.3391	-0.5425	0.0616	-0.5017	0.0599	0.0384	0.0168	0.0913	0.0234	0.1541	1.6678	36.6122	21.3751
17	4.3276	-0.7567	0.3801	15.6965	6.7837	12.4815	0.0485	0.1524	1.5845	0.7778	0.0973	-0.4291	-0.0876	-0.0174	-0.1457	0.0941	-0.01	-0.04	0.0787	0.0543	0.4406	37.6593	24.0983	24.465
18	24.7855	-8.1676	-0.1343	2.1989	1.6128	9.8786	-0.3934	0.4683	-0.1867	0.249	-0.0883	0.0236	0.4931	0.4416	0.4817	0.0902	0.0453	0.0375	0.0987	0.0566	0.1973	2.5683	23.0091	24.4506
19	1.0791	-0.8661	0.6791	2.7565	-0.7112	6.3889	-0.0555	0.0077	0.0267	0.0835	-0.1403	-0.328	0.0706	0.4488	0.1958	0.0211	-0.0011	0.0087	0.0663	0.027	0.1051	36.3017	21.2966	19.5464
20	2.7859	0.6075	-3.6538	5.1264	-1.2799	4.1443	-0.0699	-0.0973	-0.0056	0.2621	0.0903	0.2867	-0.0036	0.0839	-0.0204	0.0473	0.0427	0.001	0.0885	0.0333	0.0821	4.137	28.4677	25.6374
21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.079	0	0	0.079	0	0.079	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 - 19
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
25	X-RAY DIFFRACTION	21	A	101

-
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