PDB-3mxd: Crystal structure of HIV-1 protease inhibitor KC53 in complex wit...

ID or keywords:

Entry

Database: PDB / ID: 3mxd

Title

Crystal structure of HIV-1 protease inhibitor KC53 in complex with wild-type protease

Components

HIV-1 protease

Keywords

HYDROLASE/HYDROLASE INHIBITOR / drug design / HIV-1 protease / protease inhibitors / HYDROLASE-HYDROLASE INHIBITOR complex

Function / homology

Function and homology information

HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...
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)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

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

Citation

Journal: J.Med.Chem. / Year: 2010
Title: Structure-Based Design, Synthesis, and Structure-Activity Relationship Studies of HIV-1 Protease Inhibitors Incorporating Phenyloxazolidinones.
Authors: Ali, A. / Reddy, G.S. / Nalam, M.N. / Anjum, S.G. / Cao, H. / Schiffer, C.A. / Rana, T.M.

History

Deposition	May 7, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 10, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 6, 2021	Group: Database references / Derived calculations / Structure summary Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Sep 6, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4	Mar 13, 2024	Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3mxd.cif.gz	95.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3mxd.ent.gz	75.2 KB	Display	PDB format
PDBx/mmJSON format	3mxd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3mxd_validation.pdf.gz	754 KB	Display	wwPDB validaton report
Full document	3mxd_full_validation.pdf.gz	754.4 KB	Display
Data in XML	3mxd_validation.xml.gz	11.1 KB	Display
Data in CIF	3mxd_validation.cif.gz	15.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mx/3mxd ftp://data.pdbj.org/pub/pdb/validation_reports/mx/3mxd	HTTPS FTP

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Related structure data

Related structure data	3mxeC 1f7aS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4qlh-d 4dqh-d 4fe6-1 3o9a-d 2qi4-d 4njs-2 3bgc-d 1bv9-d 1mer-d 1dmp-d 3o99-d 1t7j-d 1mrw-d 4gb2-d 3o9i-d 1meu-d 6bz2-d 3nuj-d 1xl5-d 3sa7-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: HIV-1 protease

B: HIV-1 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)	50.674, 57.858, 61.914
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	HIV-1 protease / Protease / Retropepsin / PR Mass: 10815.790 Da / Num. of mol.: 2 / Fragment: residues 491-589 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Strain: SF2 / Gene: gag-pol / Plasmid: PXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP56 / References: UniProt: P03369, HIV-1 retropepsin
#2: Chemical	ChemComp-K53 / (5S)-N-{(1S,2R)-3-[(1,3-benzodioxol-5-ylsulfonyl)(2-methylpropyl)amino]-1-benzyl-2-hydroxypropyl}-3-(2-hydroxyphenyl)-2 -oxo-1,3-oxazolidine-5-carboxamide / (5S)-N-[(1S,2R)-3-[(1,3-Benzodioxol-5-ylsulfonyl)(2-methylpropyl)amino]-2-hydroxy-1-(phenylmethyl)propyl]-3-(2-hydroxyp henyl)-2-oxooxazolidine-5-carboxamide Mass: 625.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₁H₃₅N₃O₉S / Details: synthesized in the laboratory
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 114 / 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: 41.37 %
Crystal grow	Temperature: 298 K / pH: 6.2 Details: 126 mM sodium phosphate pH 6.2, 63 mM sodium citrate, 24-29% ammonium sulphate, 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
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 28, 2007 / 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: 13809 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / R_merge(I) obs: 0.102 / R_sym value: 0.102 / Net I/σ(I): 8.3

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1F7A

1f7a

Resolution: 1.95→39.22 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.948 / SU B: 6.484 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20087	689	5 %	RANDOM
R_work	0.16497	-	-	-
obs	0.16677	13080	99.57 %	-
all	-	13080	-	-

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: 21.641 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.39 Å²	0 Å²	0 Å²
2-	-	0.21 Å²	0 Å²
3-	-	-	0.18 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→39.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1486	0	68	114	1668

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	1549
X-RAY DIFFRACTION	r_angle_refined_deg	1.34	2.025	2245
X-RAY DIFFRACTION	r_angle_other_deg	0.711	3	3592
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.05	5	208
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.759	25.088	57
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.223	15	264
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.619	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	262
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	1803
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	294
X-RAY DIFFRACTION	r_nbd_refined	0.178	0.2	223
X-RAY DIFFRACTION	r_nbd_other	0.18	0.2	1523
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	754
X-RAY DIFFRACTION	r_nbtor_other	0.081	0.2	931
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.134	0.2	91
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	0.146	0.2	16
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.195	0.2	61
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.119	0.2	15
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	0.494	1.5	1084
X-RAY DIFFRACTION	r_mcbond_other	0.103	1.5	424
X-RAY DIFFRACTION	r_mcangle_it	0.71	2	1654
X-RAY DIFFRACTION	r_scbond_it	1.015	3	672
X-RAY DIFFRACTION	r_scangle_it	1.509	4.5	591
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→1.999 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.242	45	-
R_work	0.172	917	-
obs	-	-	96.88 %

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	3.273	-0.1494	-0.1264	5.2074	2.4907	3.0561	-0.1402	-0.3143	0.0809	0.1461	0.0676	0.1253	0.0476	0.1278	0.0726	-0.0086	0.0529	0.0178	-0.0283	0.009	-0.1265	21.06	25.8178	29.3366
2	6.1687	-3.2655	0.4013	3.2955	1.1585	5.6276	-0.1713	-0.0454	-0.5251	0.1964	0.1356	0.4093	0.2648	-0.0235	0.0357	-0.0546	-0.0025	0.0478	-0.1301	0.0512	-0.0358	19.642	17.7024	23.2464
3	4.7742	1.786	0.1228	4.1585	-1.1863	1.682	-0.0028	-0.0434	-0.0771	0.0781	-0.0936	-0.1318	-0.1297	0.021	0.0964	-0.0496	0.017	-0.0184	-0.0704	0.0136	-0.0691	27.6296	28.2638	18.9479
4	4.659	-0.998	0.8961	4.613	-0.5711	2.0019	0.0985	0.0926	-0.1812	-0.1187	-0.0187	0.2212	-0.0175	-0.0568	-0.0797	-0.0468	0.0047	0.0139	-0.0755	0.0091	-0.0591	12.739	26.7475	18.5947
5	12.5208	2.313	-0.8103	9.7975	-3.712	8.7896	-0.0477	-0.2685	-0.3973	0.3848	-0.3907	-1.4422	-0.1557	0.6005	0.4384	-0.0469	-0.0297	-0.1273	-0.1044	0.1018	0.117	39.0283	30.3612	23.7332
6	27.7965	-8.0534	1.9792	10.2789	-2.6185	13.5278	0.3414	-0.07	-0.5166	0.1276	0.0555	1.4152	-0.2186	-0.8204	-0.3969	-0.0642	-0.0404	0.024	-0.0551	0.0133	0.1995	1.7369	21.7068	18.3523
7	7.5248	0.3837	1.0788	2.6142	4.2919	7.0731	0.112	0.2341	0.2948	-0.2097	0.1154	-0.3949	-0.1294	0.4287	-0.2274	-0.0415	-0.0127	0.0229	-0.0391	0.0766	-0.0449	39.4324	30.9872	10.4068
8	7.5476	-1.6387	-0.7046	7.015	2.4796	2.54	0.1641	0.1492	-0.1003	0.024	-0.0432	0.3308	0.1701	-0.4786	-0.1208	-0.0554	-0.0286	-0.0101	0.0104	0.0905	-0.0312	0.4435	33.9492	13.5577
9	18.5181	-1.9878	-2.5013	0.4845	-0.2577	4.0563	0.0026	-0.1434	-0.096	-0.1792	-0.017	0.0055	0.0202	0.0985	0.0144	-0.019	0.0063	0.0049	-0.0978	-0.0065	-0.098	27.1402	30.7589	4.6174
10	11.1685	-2.5052	-2.1642	3.0424	-1.8058	2.5359	0.1909	0.2059	-0.0347	0.0465	-0.0306	0.1257	-0.0043	-0.0374	-0.1603	-0.0157	0.0002	-0.0022	-0.0252	-0.0111	-0.0496	12.963	38.9157	11.6008
11	0.6749	-1.537	0.3892	4.9421	1.4798	4.1072	0.0779	0.0003	0.1081	0.1421	-0.066	0.2887	-0.4443	-0.0341	-0.0119	-0.0337	-0.0188	0.0026	-0.022	0.0161	-0.0212	29.2119	32.7552	14.6402
12	9.9758	-6.0554	5.4961	8.8209	-6.6757	5.1955	0.346	0.5317	-0.1925	-0.299	-0.1517	0.36	0.28	0.3304	-0.1943	-0.0282	0.0026	-0.03	-0.0697	0.0065	-0.0275	10.5002	29.1506	12.7024
13	2.225	-1.7915	-0.3718	3.0512	-0.8497	0.8828	-0.0039	0.2067	-0.1095	0.1551	-0.0611	-0.1125	0.0735	0.2213	0.065	-0.0089	-0.0001	0.0096	-0.0293	0.0111	0.0033	28.924	19.615	19.7513
14	8.6595	-0.0988	-7.0405	1.6978	-0.9432	6.3417	-0.4267	-0.5027	-0.0712	0.0088	0.3769	0.3497	0.0863	0.0586	0.0498	-0.0102	0.0419	0.0351	-0.0019	0.0336	-0.022	11.7742	28.6182	27.049
15	2.5015	-2.4854	2.8773	14.9801	-21.7368	31.7955	0.3246	0.2335	-0.7568	-0.8347	-0.9287	-0.3688	0.2274	0.9117	0.6041	-0.0762	0.0717	0.0533	-0.0238	0.0446	0.0482	38.9434	23.0426	10.525
16	12.0102	10.374	-6.672	12.2227	-11.4837	16.9659	0.4781	-0.1992	0.5342	0.558	0.2452	0.5084	-0.586	-0.0581	-0.7233	-0.1146	0.0553	0.0279	-0.0788	0.0729	0.0838	1.4301	36.3255	21.07
17	19.8972	2.8785	-4.6614	9.353	-6.6958	19.989	-0.4115	-0.6274	0.9301	0.5496	0.0192	-0.2319	0.0834	0.6744	0.3923	-0.0965	-0.0636	-0.1161	-0.1223	0.0345	0.0585	37.1767	24.1664	23.8849
18	38.5749	-25.4262	12.3605	24.4568	-6.453	7.8068	-0.1127	1.1215	-0.3776	0.542	-0.5622	-0.1244	0.4475	0.4767	0.6749	-0.0175	0.053	0.0897	0.0298	0.0881	0.0204	3.2844	23.2928	24.3419
19	2.0255	0.0217	-0.1752	2.9001	-1.2976	2.3756	-0.0038	0.0639	-0.1073	-0.0296	-0.1417	-0.2419	0.0292	0.1207	0.1455	-0.0475	0.0056	0.0166	-0.0623	0.0272	-0.0034	35.8274	21.8564	17.5027
20	2.7861	3.2878	-5.4581	6.1227	-6.0418	10.7639	0.0592	-0.1405	-0.0781	-0.3296	0.1079	0.4466	0.1016	0.2435	-0.1671	-0.0643	0.0372	-0.0172	-0.0055	0.0743	0.0552	4.2179	29.5411	24.9154
21	3.0248	1.9633	-1.3379	5.4293	-0.1405	5.1369	0.1844	0.1105	-0.1929	-0.2788	-0.0205	0.2023	-0.1793	-0.1615	-0.1639	-0.0689	0.0173	-0.0089	-0.0531	0.0174	-0.1082	19.9099	29.8152	13.4408

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	C	200

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