PDB-2qhz: Crystal structure of protease inhibitor, MIT-1-AC87 in complex wi...

ID or keywords:

Entry

Database: PDB / ID: 2qhz

Title

Crystal structure of protease inhibitor, MIT-1-AC87 in complex with wild type HIV-1 protease

Components

Protease

Keywords

HYDROLASE / Drug design / HIV-1 protease / protease inhibitors

Function / homology

Function and homology information

HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...
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: 1.85 Å

Authors

Schiffer, C.A. / Nalam, M.N.L.

Citation

Journal: J.Am.Chem.Soc. / Year: 2008
Title: HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants.
Authors: Altman, M.D. / Ali, A. / Reddy, G.S. / Nalam, M.N. / Anjum, S.G. / Cao, H. / Chellappan, S. / Kairys, V. / Fernandes, M.X. / Gilson, M.K. / Schiffer, C.A. / Rana, T.M. / Tidor, B.

History

Deposition	Jul 3, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 22, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.2	Oct 18, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3	Oct 20, 2021	Group: Advisory / Database references / Derived calculations Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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 1.4	Aug 30, 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	2qhz.cif.gz	58.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2qhz.ent.gz	43.7 KB	Display	PDB format
PDBx/mmJSON format	2qhz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2qhz_validation.pdf.gz	780.5 KB	Display	wwPDB validaton report
Full document	2qhz_full_validation.pdf.gz	781.2 KB	Display
Data in XML	2qhz_validation.xml.gz	11.9 KB	Display
Data in CIF	2qhz_validation.cif.gz	16.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qh/2qhz ftp://data.pdbj.org/pub/pdb/validation_reports/qh/2qhz	HTTPS FTP

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Related structure data

Related structure data	2qhyC 2qi0C 2qi1C 2qi3C 2qi4C 2qi5C 2qi6C 2qi7C 1f7aS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2qi5-d 4njs-1 6pjm-d 3o9c-d 3hlo-d 1a94-1 1b6l-d 4obj-d 1k6t-d 5bry-d 3oy4-d 3bxr-d 3sac-d 4zls-d 4mc2-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) #163 - Jul 2013 HIV Capsid similarity (1)

Deposited unit

A: Protease

B: Protease

hetero molecules

22.7 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)	50.737, 58.011, 61.840
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 / Mutation: Q7K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: SF2 / Gene: pol / Plasmid: PXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP56 / References: UniProt: O38732, UniProt: P03369*PLUS
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-MZ2 / (2E)-N-[(1S,2R)-1-BENZYL-2-HYDROXY-3-{(2-THIENYLMETHYL)[(2,4,5-TRIFLUOROPHENYL)SULFONYL]AMINO}PROPYL]-4,4,4-TRIFLUORO-3-METHYLBUT-2-ENAMIDE Mass: 606.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₆H₂₄F₆N₂O₄S₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 166 / 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: 41.49 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 126 mM Sodium Phosphate, 63 mM sodium citrate, 24-29% ammonium sulphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 200 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 22, 2005 / Details: osmic mirrors
Radiation	Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.85→50 Å / Num. obs: 15443 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / R_merge(I) obs: 0.065 / R_sym value: 6.5 / Net I/σ(I): 12.3

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 1F7A

1f7a

Resolution: 1.85→42.3 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.945 / SU B: 5.182 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.154 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20521	777	5 %	RANDOM
R_work	0.16558	-	-	-
all	0.16749	14637	-	-
obs	0.16749	14637	95.48 %	-

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: 21.822 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.46 Å²	0 Å²	0 Å²
2-	-	0.34 Å²	0 Å²
3-	-	-	1.11 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→42.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1506	0	65	166	1737

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	1637
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1551
X-RAY DIFFRACTION	r_angle_refined_deg	1.227	2.028	2235
X-RAY DIFFRACTION	r_angle_other_deg	0.717	3	3609
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.007	5	204
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.302	24.737	57
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.353	15	282
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.454	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	257
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1770
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	293
X-RAY DIFFRACTION	r_nbd_refined	0.175	0.2	212
X-RAY DIFFRACTION	r_nbd_other	0.178	0.2	1519
X-RAY DIFFRACTION	r_nbtor_refined	0.163	0.2	729
X-RAY DIFFRACTION	r_nbtor_other	0.078	0.2	952
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	112
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	0.107	0.2	16
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.182	0.2	87
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.114	0.2	25
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	0.479	1.5	1077
X-RAY DIFFRACTION	r_mcbond_other	0.098	1.5	420
X-RAY DIFFRACTION	r_mcangle_it	0.658	2	1633
X-RAY DIFFRACTION	r_scbond_it	1.05	3	694
X-RAY DIFFRACTION	r_scangle_it	1.614	4.5	602
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.85→1.898 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.342	48	-
R_work	0.202	833	-
obs	-	-	76.08 %

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	3.4009	-1.4151	-0.2619	6.6502	1.0713	3.0889	-0.1197	-0.1427	0.0893	0.217	0.0249	0.0077	-0.0724	-0.0217	0.0948	-0.0528	0.0294	-0.0028	-0.0617	-0.0036	-0.1479	21.1366	25.7143	29.4507
2	4.7124	-1.9309	0.9613	2.5669	1.5718	6.2159	-0.1441	-0.0223	-0.4202	0.1611	0.1599	0.2319	0.2047	0.0493	-0.0158	-0.0556	-0.0081	0.0412	-0.1367	0.0449	-0.0511	19.7764	17.6864	23.0707
3	1.9826	1.7044	0.7591	2.5521	0.0928	1.273	-0.0656	0.0454	-0.0063	-0.0026	0.0181	-0.0565	-0.0682	-0.1629	0.0475	-0.0542	0.0103	-0.0101	-0.0917	-0.0015	-0.0701	27.6853	28.4526	19.241
4	5.6058	0.9405	1.7195	5.8487	0.1568	1.0011	-0.0303	0.0611	-0.1061	-0.1841	0.1149	0.0243	-0.0802	-0.0453	-0.0846	-0.0723	0.0022	0.0068	-0.087	0.004	-0.1019	12.806	26.8062	18.6671
5	12.8455	2.5564	-2.5039	4.888	-0.899	7.424	0.1479	-0.1254	0.0529	0.2182	-0.1578	-0.6493	0.0263	0.3584	0.0099	-0.0833	0.0007	-0.0631	-0.1308	0.0489	-0.0095	39.0011	30.4809	24.2812
6	33.5676	-11.1243	0.4033	4.8593	0.5588	2.729	0.2861	0.374	-0.6617	0.0487	-0.3071	0.3056	-0.1014	-0.2726	0.0211	-0.0822	-0.0174	0.0233	-0.1044	0.0022	-0.0031	1.7285	21.5981	17.9849
7	5.7652	-3.0766	-1.5511	3.1339	3.3458	8.084	-0.0098	0.1771	0.1754	0.0179	0.0376	-0.1362	0.0731	0.166	-0.0278	-0.0794	-0.0341	0.0149	-0.0824	0.0495	-0.0701	39.267	31.0237	10.1738
8	9.9205	-2.1258	-1.1349	8.2456	2.3915	4.4727	0.1433	0.1687	0.1513	0.008	-0.0681	0.06	0.0039	-0.3013	-0.0752	-0.1132	-0.0145	-0.01	-0.0718	0.0797	-0.1104	0.5933	34.8086	14.2025
9	15.8928	-3.0555	-3.2696	0.803	-0.1182	3.2598	-0.0973	0.1666	-0.1226	-0.0188	-0.0223	0.0193	-0.0222	-0.0644	0.1196	-0.0441	0.0003	0.0071	-0.1298	-0.0022	-0.0792	27.2838	30.8878	4.8032
10	11.8998	-2.2799	-3.6778	3.042	-0.5325	1.7241	0.0502	0.1006	-0.0544	-0.0801	0.0167	0.0916	-0.0346	-0.0207	-0.067	-0.0513	0.0074	0.0026	-0.0805	0.0031	-0.079	12.6056	39.4016	11.5873
11	0.8946	-0.1035	-1.8641	3.3677	-2.4358	5.9793	0.0562	0.1442	0.0971	0.0855	0.1309	0.3654	-0.2832	-0.0702	-0.1871	-0.0551	-0.0059	-0.0275	-0.0755	0.0083	-0.0511	29.1768	33.0363	15.1024
12	4.1297	-5.2709	5.9346	7.0738	-7.7131	8.5837	0.2819	0.2208	-0.0548	-0.1961	-0.122	0.297	0.3736	0.3171	-0.16	-0.0403	-0.0091	-0.0254	-0.0699	0.0061	-0.0775	10.5001	29.4254	12.8422
13	2.1654	0.4451	-0.2825	1.0169	0.5851	1.6631	0.1235	0.0262	-0.0678	0.0552	-0.1278	-0.1447	-0.0326	-0.068	0.0043	-0.0553	-0.0088	-0.0126	-0.0672	0.0023	-0.0592	29.0138	19.7347	19.7063
14	5.2314	-1.6212	-5.2301	0.5024	1.6209	5.2288	-0.2197	-0.4336	0.1197	-0.1319	0.2394	0.038	0.2089	0.045	-0.0198	-0.0544	0.0402	-0.0087	-0.0286	0.0119	-0.0554	11.7342	28.484	27.1366
15	2.1553	-1.6242	3.3681	11.265	-7.7751	21.9214	-0.0703	0.4158	-0.7478	-0.13	-0.4114	-0.0469	0.079	0.766	0.4818	-0.1431	0.0342	0.0603	-0.0483	0.051	-0.039	39.0976	23.6742	10.6768
16	14.1287	6.7578	-8.3903	13.4074	-13.1636	17.4821	0.4678	-0.3883	0.5311	0.3562	0.0655	0.6526	-0.3791	0.0664	-0.5333	-0.1445	0.0604	-0.0004	-0.1107	0.0262	-0.013	1.4067	36.2727	21.2704
17	8.5456	-3.7299	-8.839	9.7432	4.4559	24.9692	0.04	0.053	0.5118	0.1567	0.0162	-0.2053	-0.2597	0.0848	-0.0562	-0.1207	-0.0458	-0.0797	-0.123	0.0087	-0.0501	37.0976	24.4673	24.0602
18	30.4954	-15.3794	-3.4204	14.3136	4.1864	12.0281	-0.0657	0.5322	0.3949	0.0966	-0.2841	-0.7949	0.3882	0.2138	0.3498	-0.1394	0.0096	0.0259	-0.0283	0.068	-0.0836	3.2268	23.4769	24.0259
19	2.9624	-0.4744	-1.2869	3.7025	-1.3266	7.6785	-0.0094	0.0832	-0.1205	0	-0.0571	-0.26	0.1171	0.6689	0.0664	-0.0982	-0.008	0.0014	-0.1148	0.0001	-0.0225	36.3901	21.9044	18.3257
20	4.7772	2.351	-4.5924	9.5724	-4.9755	8.8633	0.0349	-0.0961	0.0447	0.0264	0.1761	0.4017	0.0324	-0.0062	-0.211	-0.1258	0.0143	-0.0371	-0.0752	0.0189	-0.0543	4.2291	29.4279	24.9452
21	9.1695	-0.6532	-1.4462	12.45	-2.1212	8.1867	0.0525	0.0616	-0.1762	-0.3491	-0.0658	-0.3872	0.1013	0.3518	0.0133	-0.0475	0.0275	-0.0018	-0.0457	0.0088	-0.0693	19.7932	30.7072	14.1875

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	20 - 32
8	X-RAY DIFFRACTION	4	B	20 - 32
9	X-RAY DIFFRACTION	5	A	11 - 19
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	200

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