PDB-4obk: Crystal structure of inactive HIV-1 protease in complex with the ...

ID or keywords:

Entry

Database: PDB / ID: 4obk

Title

Crystal structure of inactive HIV-1 protease in complex with the P1-P6 substrate variant (L449F/S451N)

Components

HIV-1 Protease
p1-p6 peptide

Keywords

HYDROLASE / Co-evolution / Resistance

Function / homology

Function and homology information

viral budding via host ESCRT complex / 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 ...
Similarity search - Function

Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...
Similarity search - Domain/homology

Biological species

Human immunodeficiency virus type 1

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.65 Å

Authors

Kolli, M.

Citation

Journal: J.Virol. / Year: 2014
Title: HIV-1 protease-substrate coevolution in nelfinavir resistance.
Authors: Kolli, M. / Ozen, A. / Kurt-Yilmaz, N. / Schiffer, C.A.

History

Deposition	Jan 7, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 26, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4obk.cif.gz	91 KB	Display	PDBx/mmCIF format
PDB format	pdb4obk.ent.gz	70.1 KB	Display	PDB format
PDBx/mmJSON format	4obk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4obk_validation.pdf.gz	470.2 KB	Display	wwPDB validaton report
Full document	4obk_full_validation.pdf.gz	473.4 KB	Display
Data in XML	4obk_validation.xml.gz	12.4 KB	Display
Data in CIF	4obk_validation.cif.gz	16.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ob/4obk ftp://data.pdbj.org/pub/pdb/validation_reports/ob/4obk	HTTPS FTP

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Related structure data

Related structure data	4obdC 4obfC 4obgC 4obhC 4objC 1t3rS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1w5v-d 2azc-d 1zsf-d 5dgu-d 1f7a-d 2xye-d 1w5x-d 5ah9-d 4mc9-d 4qj8-1 1k2c-d 3gi4-d 2i4d-d 1ebk-1 6vod-d 3oxx-1 4a6b-d 3nu6-d 4qj8-2 4qj7-1 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) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #163 - Jul 2013 HIV Capsid similarity (3) #87 - Mar 2007 Zinc Fingers similarity (2)

Deposited unit

A: HIV-1 Protease

B: HIV-1 Protease

C: p1-p6 peptide

hetero molecules

23.3 kDa, 3 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)	50.945, 58.412, 61.457
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein	HIV-1 Protease / PR / Retropepsin Mass: 10814.805 Da / Num. of mol.: 2 / Mutation: Q7K, V64I, D25N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: group M subtype B (isolate ARV2/SF2) / Gene: gag-pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106 / References: UniProt: P03369, HIV-1 retropepsin
#2: Protein/peptide	p1-p6 peptide Mass: 1234.366 Da / Num. of mol.: 1 / Mutation: L6F, S8N / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P03349

#1: Protein

HIV-1 Protease / PR / Retropepsin

Mass: 10814.805 Da / Num. of mol.: 2 / Mutation: Q7K, V64I, D25N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Human immunodeficiency virus type 1 / Strain: group M subtype B (isolate ARV2/SF2) / Gene: gag-pol / Plasmid: pXC35 / Production host:

Escherichia coli (E. coli) / Strain (production host): TAP106 / References: UniProt: P03369, HIV-1 retropepsin

#2: Protein/peptide

p1-p6 peptide

Mass: 1234.366 Da / Num. of mol.: 1 / Mutation: L6F, S8N / Source method: obtained synthetically / Source: (synth.)

Human immunodeficiency virus 1 / References: UniProt: P03349

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Non-polymers , 4 types, 150 molecules

#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 145 / 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 Å³/Da / Density % sol: 38.49 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.0M Ammonium sulphate, 0.1M Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.033 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 9, 2009 / Details: Mirrors
Radiation	Monochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033 Å / Relative weight: 1
Reflection	Resolution: 1.65→50 Å / Num. obs: 22293 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7 % / R_sym value: 0.086 / Net I/σ(I): 20.22
Reflection shell	Resolution: 1.65→1.71 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 5.39 / R_sym value: 0.414 / % possible all: 98.1

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing
REFMAC	5.5.0102	refinement
PDB_EXTRACT	3.14	data extraction
BioCARS-developed	GUI	data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1T3R

1t3r

Resolution: 1.65→30.73 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.931 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.026 / SU ML: 0.062 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21081	1146	5.2 %	RANDOM
R_work	0.17997	-	-	-
obs	0.18155	21058	97.7 %	-

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: 16.85 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.02 Å²	-0 Å²	0 Å²
2-	-	-0.07 Å²	0 Å²
3-	-	-	1.1 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→30.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1573	0	26	145	1744

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	1665
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1680
X-RAY DIFFRACTION	r_angle_refined_deg	1.589	1.987	2269
X-RAY DIFFRACTION	r_angle_other_deg	0.708	3	3854
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.557	5	219
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.82	24.603	63
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.77	15	277
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.571	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	269
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	1876
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	358
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	1.317	0.974	844
X-RAY DIFFRACTION	r_mcbond_other	1.211	0.966	842
X-RAY DIFFRACTION	r_mcangle_it	2.007	1.442	1052
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.494	1.32	821
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.65→1.692 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.23	83	-
R_work	0.178	1452	-
obs	-	-	94 %

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	1.2637	1.7901	1.5323	3.4048	0.782	4.0788	-0.2008	0.0907	0.0457	-0.2851	0.1565	0.0718	-0.2387	0.0668	0.0443	0.0511	-0.0192	-0.0096	0.0281	0	0.01	20.8063	8.6829	1.9871
2	4.6426	-0.5139	4.5269	0.3038	0.2922	7.0115	-0.0775	0.2418	-0.2261	0.066	-0.0117	0.1097	0.1731	0.2619	0.0892	0.1328	-0.0036	0.046	0.0451	-0.0453	0.0927	21.7878	-4.3986	2.7391
3	11.0735	1.0354	-5.8865	0.0975	-0.5495	3.3393	0.1248	-0.5648	0.6273	0.0118	-0.0451	0.062	-0.0705	0.2519	-0.0797	0.0272	0.0015	0.0026	0.0571	-0.0777	0.3385	19.333	12.1921	14.7649
4	2.7	-0.9813	-0.1086	1.9878	0.223	0.2534	0.0206	0.0519	0.0369	0.0715	-0.075	0.0238	0.0602	-0.0417	0.0545	0.048	-0.0069	-0.0017	0.0374	0.0004	0.0276	26.2489	2.0964	12.7697
5	5.5017	-0.6458	-0.8418	2.7932	2.3421	2.5259	0.0673	-0.069	-0.1272	0.0681	-0.0116	-0.15	0.1176	0.2722	-0.0557	0.0307	0.0248	-0.0007	0.1473	0.0424	0.0388	39.7395	-2.194	20.5235
6	3.2383	-0.6255	-1.7694	2.9454	1.5413	1.4814	0.0125	0.0359	0.0812	0	0.029	0.0036	0.0124	-0.0089	-0.0415	0.0615	-0.0102	-0.0185	0.0323	0.0098	0.0308	14.5626	0.6808	11.2298
7	6.134	2.2127	0.517	4.7611	1.6331	2.5946	0.1758	-0.2151	0.0911	-0.0287	-0.1764	0.2813	-0.133	-0.2075	0.0006	0.0296	0.005	-0.0013	0.0513	0.022	0.042	0.6975	-5.7281	16.9135
8	9.109	1.6113	2.4936	0.2972	0.6024	2.9262	-0.0834	-0.076	-0.0005	-0.0118	0.0017	0.0053	0.0235	0.1024	0.0817	0.0483	-0.0073	-0.0037	0.0494	0.0001	0.0206	27.3424	-1.5203	27.1068
9	9.858	3.1697	1.2873	4.3453	-1.0324	0.7979	-0.0567	0.0222	-0.04	-0.0389	0.0961	0.0703	-0.0047	-0.0343	-0.0394	0.0481	-0.0073	-0.0047	0.0235	0.0019	0.025	12.466	-11.3957	18.9362
10	2.9498	2.5353	-2.9244	3.836	-4.3249	7.7412	0.1444	-0.2549	0.1107	-0.0206	-0.1133	-0.069	0.0111	0.357	-0.0311	0.041	-0.0179	-0.0012	0.0742	-0.014	0.0564	38.607	4.1866	21.6898
11	5.1652	0.7973	3.2734	1.7486	1.9257	11.1658	0.058	0.082	-0.2027	-0.1952	0.1444	-0.0927	-0.0245	0.1351	-0.2024	0.0533	-0.0042	0.003	0.0177	-0.008	0.0465	37.6351	4.867	7.3971
12	2.3498	1.1056	-1.8673	1.5304	0.657	3.8254	0.0589	-0.0819	0.0239	-0.0515	-0.0446	0.0004	-0.1572	0.056	-0.0144	0.0367	0.0085	0.0071	0.0132	0.0045	0.0616	36.0696	7.1647	13.4837
13	1.76	-2.1134	3.3661	3.6795	-3.3423	8.2054	0.1273	0.0256	-0.1296	-0.1901	0.0962	0.1428	0.3242	-0.0622	-0.2235	0.0206	-0.0197	-0.0105	0.0562	0.0201	0.063	1.7667	-7.7733	11.3561
14	4.2611	4.8517	-0.9257	6.7079	-0.88	1.221	0.0026	-0.1268	0.0123	-0.0486	-0.0444	0.0578	-0.0291	0.0837	0.0418	0.0376	-0.0059	-0.0038	0.0381	-0.0017	0.0202	3.8845	5.5277	5.9909
15	1.2599	-0.1113	1.8737	2.3082	-1.1411	3.2008	0.0008	0.0192	-0.051	-0.0578	0.0951	0.0583	0.0255	-0.0096	-0.096	0.034	-0.0017	0.0203	0.0484	0.0209	0.0336	4.4102	-0.2653	5.3818
16	1.1821	-0.2386	0.7804	4.0932	-0.1062	2.0489	0.1105	-0.0529	-0.0584	-0.0218	-0.0295	0.2088	0.1899	0.0248	-0.081	0.0408	-0.001	0.0138	0.0294	0.0085	0.0467	29.774	-4.1105	16.0463
17	5.8545	4.0898	-4.6863	7.3123	-3.9449	3.8523	0.2146	-0.3428	0.0324	0.3507	-0.1902	0.0082	-0.2023	0.2678	-0.0244	0.0441	-0.0152	-0.008	0.0318	0.0025	0.0247	10.2892	-0.1064	17.9447
18	5.8791	1.6751	-0.8504	1.1099	-1.9954	4.987	-0.0411	-0.0299	0.1319	-0.0473	-0.0396	0.002	0.0881	0.0982	0.0807	0.0461	-0.0042	0.0138	0.0044	0.0058	0.0573	29.2676	9.3357	11.3837
19	3.4121	0.6049	0.7202	3.4783	-1.9262	2.5435	-0.0121	0.1699	0.039	0.0911	0.0597	0.1389	-0.0421	-0.0673	-0.0476	0.0353	-0.0035	0.0024	0.0525	0.0026	0.016	11.9821	-0.0384	3.6236

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

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

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Non-polymers , 4 types, 150 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Phasing

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Processing

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