PDB-4eqj: Crystal Structure of inactive single chain variant of HIV-1 Prote...

ID or keywords:

Entry

Database: PDB / ID: 4eqj

Title

Crystal Structure of inactive single chain variant of HIV-1 Protease in Complex with the substrate RT-RH

Components

protease, tethered dimer
substrate RT-RH

Keywords

hydrolase/hydrolase substrate / HIV-1 protease / specificity design / drug design / Protease inhibitors / AIDS / Aspartyl protease / HYDROLASE / hydrolase-hydrolase substrate complex

Function / homology

Function and homology information

HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / 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

HIV-1 M:B_ARV2/SF2 (virus)

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Schiffer, C.A. / Mittal, S.

Citation

Journal: Protein Sci. / Year: 2012
Title: Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease.
Authors: Alvizo, O. / Mittal, S. / Mayo, S.L. / Schiffer, C.A.

History

Deposition	Apr 19, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 6, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 20, 2012	Group: Derived calculations
Revision 1.2	Jan 9, 2013	Group: Database references
Revision 1.3	Jul 26, 2017	Group: Advisory / Refinement description / Source and taxonomy Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4	Nov 15, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5	Feb 28, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4eqj.cif.gz	158.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4eqj.ent.gz	133.6 KB	Display	PDB format
PDBx/mmJSON format	4eqj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4eqj_validation.pdf.gz	462.6 KB	Display	wwPDB validaton report
Full document	4eqj_full_validation.pdf.gz	478.6 KB	Display
Data in XML	4eqj_validation.xml.gz	15 KB	Display
Data in CIF	4eqj_validation.cif.gz	21.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eq/4eqj ftp://data.pdbj.org/pub/pdb/validation_reports/eq/4eqj	HTTPS FTP

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Related structure data

Related structure data	4ep2C 4ep3C 4epjC 4eq0C C: citing same article (ref.)
Similar structure data	6oxo-d 4eq0-d 2psv-d 4djq-d 2r5q-1 6opu-d 4gb2-d 4dqb-d 2fgu-d 3o9h-d 2qi6-d 3i7e-d 6pje-d 3o9b-d 4q1y-d 2q64-d 3mxe-d 2pwr-d 3sac-d 4dqe-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, tethered dimer

G: substrate RT-RH

hetero molecules

23.5 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)	50.994, 59.286, 62.130
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

biological unit is the same as asym.

#1: Protein	protease, tethered dimer Mass: 22169.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Strain: SF2 / Gene: gag-pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03369, HIV-1 retropepsin
#2: Protein/peptide	substrate RT-RH Mass: 900.929 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Synthetic peptide corresponding to RT-RH cleavage site (HIV-1 protease) Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YV20
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.04 Å³/Da / Density % sol: 39.72 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, hanging drop, vapor diffusion, temperature 295K, VAPOR DIFFUSION, HANGING DROP

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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: Mar 9, 2009

Radiation

Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9 Å / Relative weight: 1

Reflection

Resolution: 1.8→50 Å / Num. obs: 18038 / % possible obs: 99.4 % / Redundancy: 6.1 % / R_merge(I) obs: 0.068 / Net I/σ(I): 14.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.8-1.86	6.3	0.506	1	100
1.86-1.94	6.3	0.358	1	100
1.94-2.03	6.3	0.243	1	100
2.03-2.13	6.2	0.187	1	100
2.13-2.27	6.2	0.138	1	100
2.27-2.44	6.2	0.106	1	100
2.44-2.69	6.2	0.083	1	99.9
2.69-3.08	6.1	0.071	1	100
3.08-3.88	6	0.065	1	100
3.88-50	5.4	0.041	1	94.9

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→42.89 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.938 / Occupancy max: 1 / Occupancy min: 0 / SU B: 14.597 / SU ML: 0.21 / SU R Cruickshank DPI: 0.3146 / Cross valid method: THROUGHOUT / ESU R: 0.313 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23917	919	5.1 %	RANDOM
R_work	0.19736	-	-	-
obs	0.19961	17076	99.38 %	-

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: 36.144 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.65 Å²	0 Å²	0 Å²
2-	-	-0.26 Å²	0 Å²
3-	-	-	2.91 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→42.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1556	0	30	76	1662

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	3175
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2173
X-RAY DIFFRACTION	r_angle_refined_deg	1.461	1.986	4304
X-RAY DIFFRACTION	r_angle_other_deg	1.288	3	5312
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.875	5	404
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.413	24.404	109
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.88	15	533
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.272	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	516
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	3425
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	579
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.798→1.845 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.34	48	-
R_work	0.259	1139	-
obs	-	-	99 %

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	4.9391	-2.4287	-0.3672	3.9786	2.3894	4.4101	-0.0862	-0.3664	-0.1495	0.4297	0.0302	0.1478	0.178	-0.0155	0.056	0.3242	0.0174	0.0078	0.3212	0.036	0.1205	4.8633	3.109	32.9458
2	14.2496	-2.2156	4.1074	3.8013	-0.2854	1.2299	0.085	-0.2302	-0.0888	0.1708	-0.1413	0.2726	0.0756	-0.0696	0.0563	0.3085	-0.0048	0.0632	0.2803	0.0238	0.2221	-5.5525	-2.1429	25.417
3	2.6381	1.6416	0.7429	10.2089	-0.2441	0.5206	-0.2434	0.0135	0.1343	0.0889	-0.0195	0.8304	0.0692	-0.0908	0.2629	0.2923	-0.0449	0.1042	0.3025	-0.0644	0.3842	-13.5052	-4.2235	22.6363
4	2.7141	1.4252	0.3424	1.9556	1.4536	2.2727	-0.0432	0.1547	-0.0318	0.0554	-0.0757	-0.0244	-0.005	0.0307	0.1189	0.2545	0.0251	0.012	0.2621	0.0162	0.1896	1.105	2.6168	19.0924
5	7.0321	9.8799	1.4352	15.0253	2.244	1.5623	-0.1174	0.0676	0.0605	-0.3137	-0.1924	0.2343	0.0624	-0.0482	0.3098	0.2734	0.0267	0.0024	0.2652	-0.0233	0.2091	-6.7453	-2.2477	13.3748
6	7.8659	0.2615	-1.3848	7.249	-3.0606	1.4996	-0.0774	0.32	-0.0132	-0.1015	0.3075	0.4701	0.0566	-0.1996	-0.2301	0.2702	-0.0021	0.0156	0.3269	-0.0654	0.2853	-17.9059	-1.2208	11.4993
7	13.9957	1.615	2.6505	1.2809	1.3796	2.9298	0.08	-0.0504	0.1025	-0.4438	-0.1012	-0.1697	-0.1438	-0.2989	0.0212	0.322	0.0618	0.0211	0.3155	0.0346	0.229	-9.2036	1.883	2.9145
8	8.7859	-1.841	-0.0489	0.3892	0.0136	0.0038	-0.0221	-0.2826	0.6484	0.03	0.0276	-0.1311	0.0316	-0.0105	-0.0055	0.3277	0.0112	0.0887	0.4201	0.0586	0.3743	3.2706	-2.9237	4.4451
9	2.5319	-4.7191	-2.4053	12.9718	4.7163	2.6811	0.0777	0.5106	0.1174	-0.6179	-0.2741	0.4165	-0.0089	-0.4524	0.1964	0.2801	0.0269	-0.0425	0.3856	0.0401	0.3197	-10.7453	0.3521	6.2447
10	6.1555	-2.4694	6.085	1.6951	-4.281	12.9929	-0.0032	-0.0607	0.0692	0.1838	-0.021	0.2749	-0.1612	-0.561	0.0242	0.2671	-0.0506	0.1106	0.3002	-0.1688	0.4751	-14.697	6.9335	18.5721
11	6.544	-2.2256	-0.5522	7.4517	-3.3266	4.2368	-0.2627	-0.7186	0.3486	0.4415	0.0123	0.1274	-0.3086	-0.1736	0.2504	0.2358	0.0071	-0.0019	0.2619	-0.0667	0.2274	-10.3733	7.9993	25.6084
12	4.9914	-5.8961	-4.3513	14.0725	7.1776	4.4603	-0.1471	0.3113	0.0854	-0.0079	0.0227	0.2281	0.1433	-0.1015	0.1244	0.2657	0.026	-0.0146	0.2974	-0.004	0.2028	-8.2471	0.336	10.8448
13	1.9222	0.546	-1.5311	2.2576	1.3921	3.993	-0.1406	0.1669	-0.0077	0.0551	0.02	-0.0224	0.3108	-0.0233	0.1206	0.2573	0.019	0.013	0.2089	0.0046	0.167	-1.6731	-0.1804	16.6619
14	5.0908	-2.7161	-1.0488	4.8014	0.631	1.9169	-0.0139	0.0588	0.2586	-0.1113	-0.0492	-0.1068	-0.2426	-0.1215	0.0631	0.254	0.0138	0.0091	0.2033	0.0156	0.2159	-4.7525	10.1597	19.41
15	15.8403	0.6959	6.7447	0.3288	0.6638	4.1848	0.0135	-0.5368	0.4089	0.0884	-0.0596	-0.1954	0.0277	-0.0138	0.0461	0.2917	0.0427	-0.0349	0.2244	-0.0123	0.2507	4.1751	10.9879	27.0715
16	3.898	-2.1082	4.8883	3.8522	-1.5256	6.5958	-0.32	-0.0007	0.4761	0.1879	-0.0159	-0.8444	-0.3915	-0.0267	0.3359	0.2122	0.013	-0.0289	0.1114	0.0378	0.3226	5.7744	15.2414	22.7052
17	19.5817	-6.0844	3.0728	2.6603	-2.9907	6.476	0.3099	0.4246	0.9474	0.0241	-0.0402	-0.3036	-0.3878	0.1489	-0.2697	0.0777	-0.082	0.0803	0.2003	-0.1481	0.426	16.3755	8.2828	16.6283
18	13.3292	4.4095	17.7328	1.8124	5.7366	23.6743	-1.0497	1.444	1.0687	-0.4064	0.3044	0.3404	-0.6348	1.8354	0.7453	0.2029	-0.2492	-0.0504	0.5054	-0.0635	0.9935	20.738	6.8955	14.5261
19	5.6723	-5.1672	1.7548	11.186	-1.2286	0.5706	0.0631	0.0786	-0.1831	0.0786	0.0284	0.2706	0.0215	0.0387	-0.0915	0.1766	0.0092	-0.0117	0.1558	0.0081	0.1528	8.3337	0.6099	20.8137
20	7.5748	0.8946	-7.8626	2.3229	-0.2625	8.3963	-0.2988	-0.1482	0.1554	-0.2187	0.4916	0.0718	0.3302	0.3592	-0.1928	0.2181	0.0637	-0.0439	0.2321	-0.0578	0.2019	17.413	-2.1577	13.5823
21	11.9092	1.3194	-1.3379	6.0981	-4.9836	4.1026	0.0421	-0.1125	-0.5149	-0.0561	-0.2586	-0.3967	0.0164	0.205	0.2165	0.133	0.0077	0.0486	0.2092	-0.0612	0.3071	27.4891	-6.7189	13.835
22	7.2074	-2.7764	0.0351	1.826	-0.0382	2.1453	-0.0571	0.0175	-0.3279	0.3368	0.1215	-0.0117	-0.1049	-0.0988	-0.0644	0.1838	0.0194	-0.0369	0.1285	-0.0061	0.2312	11.4836	-11.7104	12.9314
23	7.997	0.1276	4.3183	8.6048	3.2124	3.952	-0.1118	0.2216	-0.183	-0.4508	0.3965	-0.4559	-0.0265	0.1659	-0.2847	0.1302	-0.0112	0.0081	0.1728	-0.0225	0.2271	18.2139	-10.349	11.6174
24	10.8478	7.3838	7.8928	15.1562	-1.7848	10.8549	0.8198	0.1994	-0.8139	1.0566	0.1588	-0.2348	0.3047	0.2635	-0.9786	0.1133	0.1187	-0.0958	0.4631	-0.3291	0.4865	25.0784	-5.5454	21.713
25	2.6371	0.5452	-1.5384	1.2904	1.0121	19.943	-0.0175	-0.1735	0.0366	-0.0126	0.0276	-0.0714	-0.4969	0.3222	-0.01	0.0865	0.0048	-0.0068	0.1382	-0.1255	0.2892	20.9051	8.3183	24.947
26	1.7845	2.7231	5.2246	4.1984	8.1033	15.6982	-0.0763	-0.1449	0.0908	-0.0457	-0.1261	0.1047	0.0282	-0.2049	0.2025	0.2483	0.1502	-0.0962	0.2152	-0.0784	0.2883	21.8456	-1.8199	24.7502
27	3.8895	-4.5193	-1.2081	5.5735	3.0569	8.9671	0.1257	0.1166	-0.1562	-0.2325	-0.2257	0.1608	-0.3598	-0.4709	0.1	0.1535	-0.0021	0.0385	0.2251	-0.0532	0.2783	15.9899	-3.5877	9.9831
28	1.4114	-1.0555	0.0712	3.6987	-0.8516	2.0246	0.1092	0.0095	0.0988	-0.1066	0.0108	-0.3132	0.208	0.1129	-0.12	0.1718	0.0186	-0.0128	0.1742	-0.0027	0.1401	12.6202	0.2418	19.7098
29	0.7895	0.7232	-0.2692	1.6423	-1.5067	1.7133	-0.0616	0.0109	-0.2365	0.1268	0.1467	-0.0796	-0.2225	-0.148	-0.0852	0.1719	0.0594	-0.065	0.261	-0.012	0.2114	15.2102	2.3042	28.3053
30	1.1919	1.7487	-1.2266	2.7571	-1.6608	1.3775	-0.0177	0.0771	0.0214	0.1979	0.0224	-0.0085	0.1833	-0.1535	-0.0047	0.3355	0.0149	-0.0486	0.2585	-0.0309	0.1568	3.5879	8.1415	29.7786

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 6
2	X-RAY DIFFRACTION	2	A	7 - 15
3	X-RAY DIFFRACTION	3	A	16 - 21
4	X-RAY DIFFRACTION	4	A	22 - 29
5	X-RAY DIFFRACTION	5	A	30 - 35
6	X-RAY DIFFRACTION	6	A	36 - 41
7	X-RAY DIFFRACTION	7	A	42 - 47
8	X-RAY DIFFRACTION	8	A	48 - 54
9	X-RAY DIFFRACTION	9	A	55 - 60
10	X-RAY DIFFRACTION	10	A	61 - 65
11	X-RAY DIFFRACTION	11	A	66 - 72
12	X-RAY DIFFRACTION	12	A	73 - 79
13	X-RAY DIFFRACTION	13	A	80 - 87
14	X-RAY DIFFRACTION	14	A	88 - 92
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