PDB-2qi3: Crystal structure of protease inhibitor, MIT-2-AD94 in complex wi...

ID or keywords:

Entry

Database: PDB / ID: 2qi3

Title

Crystal structure of protease inhibitor, MIT-2-AD94 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 /

retroviral ribonuclease H /

exoribonuclease H /

exoribonuclease H activity / host multivesicular body / DNA integration /

RNA-directed DNA polymerase / viral penetration into host nucleus ...
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: 1.95 Å

Authors

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

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: Refinement description / Category: software
Revision 1.3	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4	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 1.5	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	2qi3.cif.gz	56.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2qi3.ent.gz	41.9 KB	Display	PDB format
PDBx/mmJSON format	2qi3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qi/2qi3 ftp://data.pdbj.org/pub/pdb/validation_reports/qi/2qi3	HTTPS FTP

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Related structure data

Related structure data	2qhyC 2qhzC 2qi0C 2qi1C 2qi4C 2qi5C 2qi6C 2qi7C 1f7aS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4djq-d 2qi6-d 2psv-d 4dqb-d 1t3r-d 6oxt-d 1mtr-d 4eq0-d 4eqj-d 3i7e-d 4q1y-d 6pjm-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

22.4 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)	50.882, 58.366, 61.839
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 / Phosphate Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-MZ5 / (2S)-N-[(1S,2R)-3-{(1,3-BENZOTHIAZOL-6-YLSULFONYL)[(2S)-2-METHYLBUTYL]AMINO}-1-BENZYL-2-HYDROXYPROPYL]-2-HYDROXY-3-METHYLBUTANAMIDE Mass: 547.730 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₇H₃₇N₃O₅S₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.12 Å³/Da / Density % sol: 42.01 %
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: Aug 22, 2006 / 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: 1.95→50 Å / Num. obs: 13691 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / R_merge(I) obs: 0.066 / R_sym value: 6.6 / Net I/σ(I): 9.9

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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: 1.95→42.45 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.946 / SU B: 6.969 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.18 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21045	683	5 %	RANDOM
R_work	0.17363	-	-	-
all	0.17552	12976	-	-
obs	0.17552	12976	98.22 %	-

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 mean: 19.813 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.99 Å²	0 Å²	0 Å²
2-	-	-0.32 Å²	0 Å²
3-	-	-	1.31 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→42.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1477	0	47	119	1643

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	1589
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1511
X-RAY DIFFRACTION	r_angle_refined_deg	1.16	2.014	2176
X-RAY DIFFRACTION	r_angle_other_deg	0.694	3	3503
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.042	5	204
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.791	25.273	55
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.213	15	255
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.087	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	259
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	1745
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	278
X-RAY DIFFRACTION	r_nbd_refined	0.178	0.2	200
X-RAY DIFFRACTION	r_nbd_other	0.172	0.2	1494
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	724
X-RAY DIFFRACTION	r_nbtor_other	0.079	0.2	970
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.112	0.2	94
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	0.132	0.2	5
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.166	0.2	44
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.14	0.2	12
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	0.422	1.5	1027
X-RAY DIFFRACTION	r_mcbond_other	0.087	1.5	420
X-RAY DIFFRACTION	r_mcangle_it	0.658	2	1627
X-RAY DIFFRACTION	r_scbond_it	0.895	3	638
X-RAY DIFFRACTION	r_scangle_it	1.417	4.5	549
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.95→2.002 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.272	50	-
R_work	0.203	890	-
obs	-	-	94.95 %

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	5.7141	-1.889	-0.6324	6.7801	1.3917	3.7987	-0.3261	-0.4088	0.0905	0.4047	0.264	-0.0124	0.1178	0.0939	0.062	-0.0467	0.0514	0.0051	-0.0325	-0.0076	-0.1827	20.9559	25.8041	29.0777
2	3.5721	-2.1165	1.584	3.2939	0.0143	2.7311	-0.17	-0.11	-0.4516	0.263	0.232	0.353	0.0261	-0.031	-0.062	-0.0365	0.0186	0.0413	-0.0987	0.0342	-0.0602	19.7717	17.8163	23.162
3	2.6535	1.8271	1.079	2.2718	-0.2746	2.2406	-0.0418	0.0293	-0.0277	0.0128	0.0517	0.0396	0.0396	0.0217	-0.0099	-0.0436	0.0257	0.0032	-0.0715	0.0051	-0.083	27.5982	28.352	18.864
4	6.8702	-1.0051	1.8839	5.3615	0.7459	1.4742	0.0586	-0.0155	-0.337	-0.1338	-0.022	0.1267	-0.095	-0.0824	-0.0366	-0.0507	0.0146	0.0207	-0.0902	0.0066	-0.0718	12.7092	26.6943	18.1115
5	20.9501	-0.4672	-5.0324	6.6829	2.7669	6.2521	-0.1362	-0.4971	-0.2647	0.1883	-0.0519	-0.7559	0.1708	0.288	0.1881	-0.047	0.0087	-0.0603	-0.1253	0.0351	-0.0346	38.8781	30.514	23.9592
6	26.2845	-10.2901	-3.1175	4.4853	2.2049	2.4912	0.1409	0.3162	-0.8492	-0.1725	-0.0497	0.3754	0.0757	-0.3688	-0.0912	-0.0611	-0.0313	0.0363	-0.0682	0.0069	0.0853	2.3816	21.9197	17.2499
7	7.7169	1.8098	1.4968	2.4322	3.8787	8.7276	0.3401	0.2852	-0.119	0.0165	0.1545	-0.6851	-0.1777	0.2698	-0.4946	-0.0727	-0.0098	0.0182	-0.1117	0.038	0.0326	39.509	31.2648	10.425
8	11.4878	-3.0665	-2.9223	11.9655	1.5093	3.7508	0.0257	0.6169	0.0757	-0.0589	0.0483	0.6628	0.2984	-0.4303	-0.074	-0.1236	-0.0204	-0.0057	-0.0547	0.0895	-0.0772	0.4424	34.0491	13.2925
9	11.5474	-1.7607	-1.0269	1.842	0.1002	3.918	-0.0862	0.2369	0.0292	-0.0066	-0.0811	0.0043	-0.0251	0.0449	0.1674	-0.0503	0.0042	0.0101	-0.089	0.0019	-0.1117	27.3248	31.2564	4.412
10	17.323	-2.707	-2.499	3.327	-1.9086	2.1807	0.1398	0.3241	-0.1419	-0.0212	0.0303	0.2752	0.0483	0.0755	-0.1701	-0.0364	0.0056	-0.003	-0.0654	-0.0033	-0.0541	12.8535	39.3419	11.1782
11	0.2447	-0.6211	-0.813	2.7728	0.0943	5.9391	-0.0422	-0.0552	0.0254	0.0685	-0.0655	0.1055	-0.3355	-0.0791	0.1078	-0.0504	-0.0189	-0.0262	-0.0516	0.0137	-0.0371	29.2418	32.9956	14.6101
12	7.2459	-7.5191	6.5813	9.0823	-5.8775	6.6859	0.2726	0.2795	-0.0727	-0.2395	-0.1871	0.0304	0.1538	0.1475	-0.0854	-0.0671	-0.0158	-0.0238	-0.0701	0.0217	-0.0722	10.4101	29.1619	12.2467
13	5.285	0.4972	2.5888	3.0664	1.2822	1.6254	-0.0587	0.1189	-0.1003	-0.0353	-0.0026	-0.0383	0.0807	-0.2177	0.0613	-0.026	0.0124	0.0075	-0.0382	0.0053	-0.0449	28.993	19.7411	19.5692
14	5.3431	-1.2973	-1.6468	0.4702	-0.5302	6.0801	-0.3161	-0.4347	0.0207	0.024	0.2212	0.3044	-0.0199	-0.1162	0.0948	-0.0205	0.0502	0.0259	-0.0412	0.006	-0.0547	11.5386	28.4519	26.6382
15	5.5505	-8.2066	2.1751	15.7847	-12.5865	24.9018	0.0788	0.0273	-0.3532	-0.2166	-0.442	-0.4387	0.1832	0.6687	0.3632	-0.152	0.0127	0.0317	0.0214	0.044	-0.0275	39.1431	23.4659	10.6206
16	14.058	7.3988	-13.2228	16.7295	-16.9085	20.1492	0.5628	-0.4321	0.9229	0.7676	0.2792	0.5245	-0.7069	0.0831	-0.842	-0.0806	0.0377	0.0128	-0.0659	-0.0051	0.013	1.3114	36.1847	20.7339
17	18.074	-1.84	-12.0899	12.0181	3.7551	33.2031	0.2005	-0.2729	0.7535	0.2431	0.283	-0.2127	0.0212	-0.308	-0.4834	-0.1012	-0.0081	-0.0613	-0.1632	-0.0102	-0.035	37.0806	24.4767	23.9589
18	19.0893	-27.7136	7.7509	51.4635	-1.5202	16.9101	0.4092	0.9042	-0.4953	-0.4762	-0.5969	0.4295	1.2035	0.4688	0.1876	-0.0997	0.023	0.0566	-0.0151	0.0666	0.0812	3.1261	23.0488	23.6148
19	4.5659	-1.098	3.3132	1.9757	1.408	5.2442	0.1327	0.0833	-0.1735	-0.07	-0.1735	-0.068	0.1927	0.2204	0.0409	-0.0772	-0.0092	0.0221	-0.0764	0.02	-0.0384	35.916	22.1095	17.5286
20	2.3191	0.9339	-3.7139	9.0203	-5.2107	10.1712	0.0689	-0.2084	-0.1105	0.1043	-0.0017	0.3012	0.0722	0.1675	-0.0673	-0.145	0.0136	-0.0033	-0.0404	0.0305	0.0087	4.1349	29.3956	24.4505
21	4.246	-8.6822	-1.2084	20.911	8.5872	12.1912	0.0794	0.1224	0.3226	0.054	0.1194	-0.2344	0.0474	0.2224	-0.1988	-0.0887	-0.0167	0.0046	-0.0927	-0.0005	-0.0799	19.6624	30.8372	14.074

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	B	200

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