PDB-3o9h: Crystal Structure of wild-type HIV-1 Protease in complex with kd26

ID or keywords:

Entry

Database: PDB / ID: 3o9h

Title

Crystal Structure of wild-type HIV-1 Protease in complex with kd26

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

: / : /

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: 1.7 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	Nov 23, 2011	Group: Structure summary
Revision 1.2	Nov 27, 2013	Group: Database references
Revision 1.3	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.4	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 1.5	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3o9h.cif.gz	95.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3o9h.ent.gz	74.7 KB	Display	PDB format
PDBx/mmJSON format	3o9h.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/o9/3o9h ftp://data.pdbj.org/pub/pdb/validation_reports/o9/3o9h	HTTPS FTP

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Related structure data

Related structure data	3o99C 3o9aC 3o9bC 3o9cC 3o9dC 3o9eC 3o9fC 3o9gC 3o9iC C: citing same article (ref.)
Similar structure data	3sac-d 2qi0-d 1tsq-d 3o9c-d 3bgc-d 4rvx-1 3gga-1 3o9b-d 3ekv-d 3qrm-d 5ah6-d 3sa6-d 6oxs-d 2psv-d 2nxd-d 1a30-d 5kr2-2 6opu-d 2fxd-d 4m8y-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)	50.735, 57.634, 61.795
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 / 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-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-K2E / (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(1S,2R)-3-[(1,3-benzodioxol-5-ylsulfonyl)(2-ethylbutyl)amino]-1-benzyl-2-hydroxypropyl}carbamate Mass: 604.712 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₀H₄₀N₂O₉S
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.09 Å³/Da / Density % sol: 41.1 %
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

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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: Jun 4, 2008

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: 20447 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / R_merge(I) obs: 0.062 / Net I/σ(I): 13

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.7-1.76	3.6	0.381	1	95.2
1.76-1.83	5.2	0.328	1	99.9
1.83-1.91	5.6	0.26	1	99.9
1.91-2.02	5.6	0.183	1	99.8
2.02-2.14	5.7	0.138	1	100
2.14-2.31	5.8	0.11	1	100
2.31-2.54	5.9	0.085	1	100
2.54-2.91	5.9	0.061	1	100
2.91-3.66	5.9	0.041	1	100
3.66-50	5.7	0.035	1	99.2

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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: 0.965 / Cor.coef. F_o:F_c free: 0.938 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.136 / SU ML: 0.069 / SU R Cruickshank DPI: 0.1096 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20849	1045	5.1 %	RANDOM
R_work	0.16629	-	-	-
obs	0.16835	19357	99.42 %	-

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: 25.81 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.9 Å²	0 Å²	0 Å²
2-	-	0.06 Å²	0 Å²
3-	-	-	0.84 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→39.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1486	0	66	155	1707

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	1611
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1070
X-RAY DIFFRACTION	r_angle_refined_deg	1.502	2.025	2203
X-RAY DIFFRACTION	r_angle_other_deg	0.863	3	2636
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.213	5	202
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.563	24.737	57
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.073	15	259
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.133	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	259
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1746
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	288
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	242
X-RAY DIFFRACTION	r_nbd_other	0.202	0.2	1104
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	747
X-RAY DIFFRACTION	r_nbtor_other	0.084	0.2	875
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.111	0.2	119
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	0.111	0.2	8
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.157	0.2	52
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.134	0.2	21
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	0.714	1.5	1068
X-RAY DIFFRACTION	r_mcbond_other	0.192	1.5	418
X-RAY DIFFRACTION	r_mcangle_it	0.9	2	1619
X-RAY DIFFRACTION	r_scbond_it	1.532	3	661
X-RAY DIFFRACTION	r_scangle_it	2.201	4.5	584
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.7→1.744 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.251	76	-
R_work	0.207	1317	-
obs	-	-	93.8 %

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	3.126	-0.08	-0.1249	3.5743	-0.1142	2.052	-0.0673	-0.179	0.0797	0.241	0.0233	0.0617	-0.0747	0.0663	0.044	-0.0139	0.0336	0.0064	-0.0217	-0.0083	-0.1039	21.0765	25.7186	29.6205
2	2.9685	-2.0508	-0.1644	2.2936	0.312	4.0172	-0.0296	0.0038	-0.2119	0.1143	0.0576	0.221	0.2243	-0.0142	-0.0279	-0.0364	0.0006	0.0252	-0.0787	0.0196	-0.0384	19.8258	17.4722	23.4246
3	3.6658	0.9815	0.9368	1.8814	-0.7401	0.846	-0.0315	0.0517	-0.0047	0.0137	-0.1205	-0.0236	-0.1087	-0.0613	0.1519	-0.0313	0.0005	-0.0039	-0.0231	0.011	-0.0583	27.8017	28.2225	18.8724
4	2.9666	-0.2306	-0.1445	4.3328	-0.6349	0.9547	0.0414	-0.0382	-0.141	-0.1774	0.0703	0.2909	-0.0031	-0.0554	-0.1118	-0.0351	0.0028	-0.0208	-0.0555	0.0164	-0.0114	12.5419	26.7406	18.7017
5	8.1625	2.7904	-4.455	5.8928	-1.9073	6.0804	-0.2122	-0.2992	-0.3768	0.2568	-0.3273	-0.9618	-0.1803	0.4001	0.5395	-0.0588	-0.0229	-0.0931	-0.0458	0.0782	0.1215	39.7759	30.3228	23.5138
6	6.999	-3.6129	2.3859	5.8655	-1.1822	5.989	0.0121	-0.2348	-0.6419	-0.1074	0.1607	0.9136	-0.1443	-0.4601	-0.1728	-0.0812	-0.0028	-0.0276	-0.0396	0.0007	0.1831	0.9856	21.8101	18.3982
7	4.393	-0.3751	0.666	2.4761	2.8991	4.9168	0.0173	0.316	0.1975	-0.046	0.0025	-0.1013	-0.1451	0.3433	-0.0198	-0.0587	-0.0219	0.0054	0.0142	0.0608	-0.0518	39.5765	31.2121	10.0447
8	7.5895	-0.5976	-0.9796	4.8196	2.3438	4.355	0.2159	0.2159	-0.0741	-0.1112	0.017	0.2225	0.159	-0.5072	-0.2328	-0.0794	-0.009	-0.0049	0.0018	0.0825	-0.0613	0.2936	34.107	13.2677
9	8.0597	-1.5038	-2.0609	0.7503	-0.2291	3.6219	0.0861	0.0681	-0.1481	-0.035	-0.0331	0.0346	-0.0756	0.1329	-0.0529	-0.0333	0.0117	0.0093	-0.0437	-0.0141	-0.0405	27.4301	30.6032	4.2868
10	9.6696	-3.3229	-1.24	3.5186	-1.4387	1.6221	0.1023	0.2812	0.229	0.0303	-0.0134	0.0733	0.0618	-0.0136	-0.0889	-0.0334	-0.0046	0.0083	-0.0249	-0.0057	-0.0428	12.6971	39.0739	11.6937
11	0.7912	0.6885	-1.8979	4.3289	-0.5505	7.3334	0.0234	0.057	0.0327	-0.1237	-0.0401	0.1413	-0.3889	-0.0378	0.0167	-0.0237	-0.0034	-0.0064	-0.0346	0.0183	-0.046	29.1405	33.1059	14.2369
12	3.5417	-4.4016	3.146	7.4507	-3.5612	3.3505	0.3765	0.3379	-0.1458	-0.4298	-0.1694	0.2346	0.3712	0.1841	-0.2071	-0.0231	0.0078	-0.035	-0.0472	0.0087	-0.0229	10.4383	29.1914	12.2275
13	2.4807	-1.5771	0.1386	3.7278	-0.522	0.9515	-0.0356	0.0629	-0.0253	-0.0594	0.0406	-0.1337	-0.015	-0.0248	-0.005	-0.0268	-0.0076	-0.0026	-0.027	-0.0052	-0.0232	28.7132	19.2646	19.4616
14	5.659	-2.1478	-3.7008	3.0235	-0.4757	4.0211	-0.2365	-0.3516	-0.1153	0.164	0.2185	0.4346	-0.1165	-0.0336	0.0181	-0.0382	0.0338	0.025	-0.0107	0.0307	-0.0087	12.036	28.9966	27.3158
15	0.9026	-3.5136	2.7821	14.0701	-13.4217	25.6802	0.2256	0.1327	-0.3467	-0.4676	-0.5848	-0.1081	0.4556	0.4919	0.3592	-0.1053	0.0378	0.0622	0.0181	0.0316	0.0084	38.81	22.7792	10.1649
16	4.8548	4.1668	-3.7433	10.1329	-4.9455	12.1475	0.2423	-0.1922	0.4516	0.3668	0.2376	0.4251	-0.4123	-0.2427	-0.4799	-0.1141	0.0441	0.0248	-0.0386	0.0648	0.0587	1.6209	36.5798	21.224
17	12.884	-0.0895	-10.4515	4.219	-2.0888	20.1083	-0.0448	-0.0603	0.6072	0.2799	0.0205	-0.1907	-0.1608	0.3706	0.0243	-0.0914	-0.0418	-0.0747	-0.0696	0.031	0.0159	37.645	24.0162	24.0979
18	11.566	-7.8773	0.8828	12.2153	2.8284	1.7844	-0.4717	0.4763	-0.6526	0.4183	0.3393	0.4643	0.4154	0.0159	0.1324	0.0138	0.034	0.0657	0.0247	0.0717	0.0521	3.0995	22.9807	24.6765
19	1.0231	-0.5098	1.8975	2.2368	-1.7479	5.2569	0.0413	0.1838	-0.0591	-0.0135	-0.0941	-0.181	0.0958	0.1665	0.0528	-0.0653	0.0077	0.0218	-0.0462	0.0225	-0.0068	35.7555	21.5913	18.2147
20	1.9135	2.0616	-4.0406	5.8065	-4.9292	8.6248	-0.1007	-0.0862	0.0676	-0.0684	0.1145	0.481	0.1784	0.1159	-0.0139	-0.0606	0.0399	0.0109	-0.0203	0.0662	0.0526	4.1454	28.5571	25.5374
21	7.9842	-5.9916	-1.5313	9.5048	1.7015	1.4828	0.092	-0.2566	0.0419	-0.0763	0.1858	-0.1135	-0.0805	0.1905	-0.2778	-0.0159	0.015	-0.0015	-0.0237	0.0018	-0.0316	19.6764	29.9748	14.1155

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 - 20
10	X-RAY DIFFRACTION	6	B	11 - 20
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	57 - 62
20	X-RAY DIFFRACTION	16	B	57 - 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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