PDB-3o9b: Crystal Structure of wild-type HIV-1 Protease in Complex with kd25

ID or keywords:

Entry

Database: PDB / ID: 3o9b

Title

Crystal Structure of wild-type HIV-1 Protease in Complex with kd25

Components

Pol polyprotein

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

viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / endonuclease activity / aspartic-type endopeptidase activity / proteolysis / DNA binding
Similarity search - Function

Biological species

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 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 27, 2013	Group: Database references
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.3	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 1.4	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3o9b.cif.gz	99.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3o9b.ent.gz	78.4 KB	Display	PDB format
PDBx/mmJSON format	3o9b.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3o9b_validation.pdf.gz	811.1 KB	Display	wwPDB validaton report
Full document	3o9b_full_validation.pdf.gz	812.4 KB	Display
Data in XML	3o9b_validation.xml.gz	12 KB	Display
Data in CIF	3o9b_validation.cif.gz	16.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o9/3o9b ftp://data.pdbj.org/pub/pdb/validation_reports/o9/3o9b	HTTPS FTP

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Related structure data

Related structure data	3o99C 3o9aC 3o9cC 3o9dC 3o9eC 3o9fC 3o9gC 3o9hC 3o9iC C: citing same article (ref.)
Similar structure data	2nxl-d 3o9h-d 3bgc-d 4gb2-d 3ekv-d 6pjf-d 6opu-d 5ivs-d 3cyw-d 4dqb-d 4q1x-d 2fgu-d 4eq0-d 2psv-d 1qbt-d 5kr2-3 2q5k-d 3sac-d 2qi0-d 4rvx-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)

Deposited unit

A: Pol polyprotein

B: Pol polyprotein

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)	50.672, 57.921, 61.746
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 , 1 types, 2 molecules AB

#1: Protein	Pol polyprotein Mass: 10815.790 Da / Num. of mol.: 2 / Fragment: HIV-1 protease (UNP residues 1 to 99) 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

#1: Protein

Pol polyprotein

Mass: 10815.790 Da / Num. of mol.: 2 / Fragment: HIV-1 protease (UNP residues 1 to 99)
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

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Non-polymers , 5 types, 175 molecules

#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-K2A / (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(1S,2R)-1-benzyl-2-hydroxy-3-({[4-(hydroxymethyl)phenyl]sulfonyl}[(2S)-2-methylbutyl]amino)propyl]carbamate Mass: 576.701 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₉H₄₀N₂O₈S
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 168 / 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: 41.27 %
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:

SYNCHROTRON / Site:

APS

/ Beamline: 14-BM-C / Wavelength: 0.9 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2009

Radiation

Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9 Å / Relative weight: 1

Reflection

Resolution: 1.5→50 Å / Num. obs: 29830 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / R_merge(I) obs: 0.067 / Net I/σ(I): 11.7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.5-1.55	7.9	0.368	1	100
1.55-1.62	7.9	0.284	1	100
1.62-1.69	7.9	0.219	1	100
1.69-1.78	7.9	0.168	1	100
1.78-1.89	7.9	0.125	1	100
1.89-2.04	7.9	0.088	1	100
2.04-2.24	7.9	0.07	1	100
2.24-2.56	7.8	0.067	1	100
2.56-3.23	7.6	0.062	1	100
3.23-50	7.1	0.036	1	98.6

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry ?

Resolution: 1.5→42.26 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.944 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 2.209 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0738 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18898	1508	5.1 %	RANDOM
R_work	0.16521	-	-	-
obs	0.16637	28263	99.82 %	-

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: 11.433 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.63 Å²	0 Å²	0 Å²
2-	-	0.21 Å²	0 Å²
3-	-	-	0.41 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→42.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1498	0	69	168	1735

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	1671
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1126
X-RAY DIFFRACTION	r_angle_refined_deg	1.266	2.025	2284
X-RAY DIFFRACTION	r_angle_other_deg	0.778	3	2786
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.135	5	214
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.284	25	56
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.354	15	283
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.586	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	267
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	1828
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	0.489	1.5	1038
X-RAY DIFFRACTION	r_mcbond_other	0.11	1.5	430
X-RAY DIFFRACTION	r_mcangle_it	0.92	2	1692
X-RAY DIFFRACTION	r_scbond_it	1.499	3	633
X-RAY DIFFRACTION	r_scangle_it	2.332	4.5	592
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.499→1.538 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.229	105	-
R_work	0.186	2066	-
obs	-	-	99.72 %

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	2.4504	-1.4906	0.1637	1.6538	0.68	2.366	-0.1032	-0.0262	-0.2145	0.1489	0.066	0.1904	0.2112	-0.0354	0.0372	0.0831	-0.0013	0.0206	0.0193	0.0122	0.0601	19.6185	17.2182	22.8379
2	2.4869	-0.9075	-0.7109	3.5416	0.9935	1.4317	-0.1535	-0.2324	0.0739	0.2351	0.1342	-0.0199	0.0277	0.1402	0.0193	0.0797	0.021	0.0025	0.0702	-0.0006	0.0051	20.888	25.8654	29.5754
3	2.3784	0.487	0.6355	1.3375	-0.4664	0.5044	-0.0113	-0.0219	-0.0274	-0.0074	0.0481	0.0332	-0.057	-0.0243	-0.0367	0.0698	0.0005	0.0076	0.0349	-0.0003	0.0495	13.805	27.6643	19.4782
4	3.0825	1.3263	0.6485	1.9926	-0.8213	1.7841	-0.0211	-0.0107	0.058	0.0455	-0.0573	0.0034	-0.0444	0.0333	0.0784	0.0485	0.0107	-0.0048	0.0445	0.0059	0.0465	26.3666	27.5007	18.5109
5	14.1123	-3.9785	-2.0807	1.1806	0.5035	0.5733	0.093	0.3384	-0.209	-0.0285	-0.1163	0.0163	0.0157	-0.1488	0.0232	0.0382	-0.024	-0.0053	0.1133	0.0181	0.0886	1.1037	21.67	17.1231
6	3.9257	-2.4884	-1.1085	1.6451	1.119	3.0165	-0.0741	-0.146	0.1201	0.0268	0.0948	-0.0951	-0.1269	0.156	-0.0207	0.047	-0.0256	-0.0401	0.0577	0.0423	0.1392	39.1866	31.2267	23.692
7	3.2521	-1.3316	-0.9071	6.4966	1.4992	1.9758	0.0245	0.1095	0.048	-0.0034	-0.0222	0.2887	-0.0092	-0.2923	-0.0023	0.03	0.0099	-0.0049	0.0965	0.043	0.0485	0.7452	35.3636	13.9686
8	3.5629	-0.1306	0.041	2.926	2.3307	3.9412	0.0362	0.0683	0.0839	-0.0539	0.109	-0.2119	-0.1087	0.3066	-0.1451	0.0349	-0.0088	0.0081	0.0583	0.0313	0.0697	39.3753	31.7408	10.3874
9	6.5988	-2.0649	-1.221	1.6591	-0.1002	0.8913	0.0703	0.0309	0.2129	-0.0583	0.0027	0.0497	-0.053	-0.0094	-0.073	0.065	0.0049	-0.006	0.0411	0.0051	0.0643	12.5422	39.6031	11.4989
10	8.267	-0.2286	-1.3086	0.0681	-0.0351	1.4968	0.0377	0.1594	-0.0173	-0.0571	0.0015	0.0113	-0.0304	0.0365	-0.0392	0.0706	0.0103	0.0019	0.0485	-0.0025	0.0352	27.561	31.056	4.3296
11	1.8745	-1.9064	2.6304	2.9787	-1.9781	4.2495	0.097	0.0827	-0.0059	-0.1497	-0.0381	0.0379	0.2064	0.167	-0.0589	0.0991	0.0105	-0.0276	0.0649	0.0043	0.0786	10.4511	29.4399	12.191
12	1.0019	0.1257	-1.1452	2.8668	-1.0184	3.2501	0.0217	0.0279	0.0558	-0.0676	0.0024	0.1762	-0.1392	-0.0129	-0.0241	0.0546	-0.0117	-0.0141	0.0446	0.0113	0.0527	28.9455	33.4707	14.4685
13	3.2756	-0.1767	-1.4047	2.1953	-0.0654	1.5678	-0.0719	-0.1912	0.0238	-0.0048	0.039	0.0841	-0.0154	-0.031	0.033	0.0625	0.0194	0.0133	0.0815	0.0053	0.0384	11.8141	28.8959	27.5652
14	2.4004	-0.37	-0.7113	2.0725	-0.6099	1.2359	0.0168	0.006	-0.0669	-0.0194	-0.0711	-0.0921	0.0778	0.0548	0.0543	0.0548	0.0073	-0.0067	0.0401	0.0043	0.0583	28.6327	19.3266	19.3924
15	7.6526	6.6167	-4.1302	8.4795	-8.6958	12.4979	0.4459	-0.1701	0.4576	0.4479	-0.0055	0.5447	-0.4745	-0.0465	-0.4403	0.0937	0.0289	0.0253	0.0813	0.0132	0.1175	1.7168	36.6772	21.4771
16	1.2438	-2.5066	4.232	8.1284	-11.3178	16.9553	0.0575	0.2068	-0.0299	-0.3845	-0.3615	-0.2509	0.3399	0.6984	0.304	0.0867	0.0387	-0.0081	0.1144	0.0237	0.2466	38.7031	23.0894	10.4627
17	14.1576	-6.2551	-0.9489	11.7532	1.5423	5.6406	-0.0877	0.3273	-0.171	-0.0354	-0.0184	0.018	0.2481	0.1267	0.1061	0.0269	0.0076	0.0008	0.0593	0.0055	0.0117	2.5653	23.0588	24.2439
18	8.2829	-0.2876	-4.6845	7.5033	1.3104	14.2919	0.0452	-0.2327	0.5762	0.3571	-0.0947	-0.2143	-0.2783	0.4464	0.0495	0.0441	-0.0268	-0.0452	0.0255	0.0122	0.1257	37.5876	24.097	24.5031
19	1.8675	1.0288	-3.3167	6.0963	-3.1765	6.2226	-0.0234	-0.0115	0.0281	0.1238	0.1164	0.2265	-0.0014	-0.0192	-0.093	0.0348	0.023	-0.0318	0.0915	0.0178	0.0695	4.1416	28.3283	25.7104
20	0.9983	-0.6833	0.8312	2.0229	-0.8231	4.9998	0.0265	0.031	-0.005	0.0613	-0.0777	-0.1905	0.1204	0.214	0.0512	0.0242	-0.0026	0.0064	0.0439	0.0177	0.0816	36.3153	21.3474	19.6527
21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.0598	0	0	0.0598	0	0.0598	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	21 - 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	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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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 175 molecules

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