PDB-2i0d: Crystal structure of AD-81 complexed with wild type HIV-1 protease

ID or keywords:

Entry

Database: PDB / ID: 2i0d

Title

Crystal structure of AD-81 complexed with wild type HIV-1 protease

Components

Protease

Keywords

HYDROLASE / Drug design / HIv-1 protease / protease inhibitors

Function / homology

Function and homology information

aspartic-type endopeptidase activity / proteolysis
Similarity search - Function

Biological species

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Nalam, M.N.L. / Schiffer, C.A. / Ali, A. / Reddy, K.K. / Cao, H. / Anjum, S.G. / Rana, T.M.

Citation

Journal: J.Med.Chem. / Year: 2006
Title: Discovery of HIV-1 Protease Inhibitors with Picomolar Affinities Incorporating N-Aryl-oxazolidinone-5-carboxamides as Novel P2 Ligands.
Authors: Ali, A. / Reddy, G.S. / Cao, H. / Anjum, S.G. / Nalam, M.N. / Schiffer, C.A. / Rana, T.M.

History

Deposition	Aug 10, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 19, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software
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

-
Download

PDBx/mmCIF format	2i0d.cif.gz	58.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2i0d.ent.gz	43.1 KB	Display	PDB format
PDBx/mmJSON format	2i0d.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2i0d_validation.pdf.gz	728.7 KB	Display	wwPDB validaton report
Full document	2i0d_full_validation.pdf.gz	729 KB	Display
Data in XML	2i0d_validation.xml.gz	6.5 KB	Display
Data in CIF	2i0d_validation.cif.gz	9.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i0/2i0d ftp://data.pdbj.org/pub/pdb/validation_reports/i0/2i0d	HTTPS FTP

-
Related structure data

Related structure data	2i0aC 1f7aS 2ioa S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3ekt-1 3ekt-2 2nxl-d 4epj-d 4djp-d 2qi1-d 5kr1-d 3ekw-d 2fgu-d 6oxy-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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#6 - Jun 2000 HIV-1 Protease 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)	50.778, 58.314, 61.693
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: O38731*PLUS
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-MUT / (5S)-3-(3-ACETYLPHENYL)-N-[(1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL]-2-OXO-1,3-OXAZOLIDINE-5-CARBOXAMIDE Mass: 637.743 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₃H₃₉N₃O₈S
#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.: 158 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.11 Å³/Da / Density % sol: 41.7 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 126mM sodium phosphate pH 6.2, 63mM sodium citrate, 27% ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
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: Feb 17, 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: 13238 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / R_merge(I) obs: 0.047 / R_sym value: 0.047 / Net I/σ(I): 11.6

-
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→42.37 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.927 / SU B: 6.992 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21588	664	5 %	RANDOM
R_work	0.1658	-	-	-
obs	0.16828	12549	95.39 %	-

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: 33.944 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.73 Å²	0 Å²	0 Å²
2-	-	-0.07 Å²	0 Å²
3-	-	-	0.8 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→42.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1494	0	69	158	1721

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	1598
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1527
X-RAY DIFFRACTION	r_angle_refined_deg	1.294	2.031	2180
X-RAY DIFFRACTION	r_angle_other_deg	0.628	3	3538
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.973	5	198
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.544	24.815	54
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.692	15	263
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.218	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	255
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1720
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	283
X-RAY DIFFRACTION	r_nbd_refined	0.186	0.2	239
X-RAY DIFFRACTION	r_nbd_other	0.187	0.2	1491
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	751
X-RAY DIFFRACTION	r_nbtor_other	0.083	0.2	978
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.17	0.2	120
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	0.137	0.2	11
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.18	0.2	60
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.117	0.2	16
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	0.812	1.5	1043
X-RAY DIFFRACTION	r_mcbond_other	0.205	1.5	414
X-RAY DIFFRACTION	r_mcangle_it	1.088	2	1599
X-RAY DIFFRACTION	r_scbond_it	1.623	3	674
X-RAY DIFFRACTION	r_scangle_it	2.269	4.5	581
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 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.234	39	-
R_work	0.191	914	-
obs	-	-	96.36 %

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	5.6552	-3.2296	1.9881	8.8408	0.1431	4.0202	-0.2898	-0.5208	0.0805	0.5905	0.1433	-0.0917	-0.0789	-0.2412	0.1465	-0.1511	0.0694	0.0311	-0.1811	-0.0141	-0.3328	20.8267	25.7255	29.1763
2	3.9611	-3.8517	1.6758	5.77	1.0341	4.2136	-0.2231	-0.0665	-0.6088	0.0878	0.2895	0.4884	0.2268	0.1243	-0.0664	-0.2236	-0.0222	0.0421	-0.2456	0.0217	-0.1656	19.5657	17.5967	22.8511
3	2.5793	1.6196	0.9585	4.5281	-0.5866	1.2177	0.038	-0.0143	0.0407	0.0833	-0.199	0.0296	-0.0022	-0.0021	0.1611	-0.213	0.0116	-0.0104	-0.1836	-0.0087	-0.218	27.4744	28.4505	18.9529
4	6.9575	-0.3495	2.5994	3.4518	-0.6461	3.3715	-0.1176	-0.174	-0.2274	-0.0842	0.1842	0.2685	-0.1021	-0.0471	-0.0666	-0.2237	0.0262	0.016	-0.2309	0.0256	-0.1864	12.5629	26.7702	18.3628
5	6.384	7.0844	-5.514	15.1341	1.2873	12.3053	-0.0834	-0.4213	-0.3295	0.112	-0.0506	-1.0061	0.3205	0.4617	0.134	-0.219	0.0188	-0.1076	-0.2212	0.0683	-0.0878	38.7734	30.4927	23.9973
6	44.5422	-24.358	-9.0655	14.8263	3.5816	10.983	-0.493	0.0747	-1.4433	0.5518	0.1376	0.9413	0.0712	-0.7034	0.3554	-0.2862	-0.0414	0.0175	-0.2388	0.0185	-0.087	1.5123	21.597	17.7563
7	5.8002	0.2245	-0.9532	7.821	7.0254	6.9944	0.3303	-0.1172	-0.3412	-0.2527	0.1516	-0.5299	-0.5585	0.5434	-0.4818	-0.2169	0.013	-0.0158	-0.2034	0.0448	-0.1763	39.4723	31.4994	10.5717
8	9.7452	-1.0745	-1.3601	12.0878	5.3574	4.2282	0.2559	0.263	0.3081	0.0632	-0.1605	0.4553	0.3359	-0.5148	-0.0954	-0.2544	-0.0146	-0.0315	-0.1868	0.1155	-0.1705	0.3556	34.3046	13.5504
9	19.8189	-1.3434	-3.1173	3.4667	-0.6866	2.3825	-0.0205	0.1943	0.1404	-0.2408	-0.0959	-0.1845	0.009	-0.1922	0.1164	-0.2063	0.023	-0.0147	-0.229	0.0003	-0.2232	27.3493	31.1744	4.54
10	17.2254	-4.1158	-2.9765	4.6244	-1.3421	1.7113	0.1931	0.5137	0.2632	-0.0937	0.13	0.2136	-0.1275	-0.0423	-0.3231	-0.1798	0.0151	-0.0132	-0.2106	0.0289	-0.1854	12.7368	39.4201	11.5806
11	0.5152	0.6918	-1.5631	2.6089	-0.0492	7.2437	0.0044	0.0743	0.1593	-0.0085	-0.0541	0.2597	-0.2031	-0.1591	0.0497	-0.2132	-0.0132	-0.0055	-0.1857	0.0186	-0.1563	29.1165	33.0542	14.7496
12	9.1101	-7.951	8.9156	10.2904	-9.3145	9.4268	0.2243	0.2089	-0.2415	-0.2135	0.0205	0.3939	0.2111	0.2054	-0.2449	-0.2341	-0.0206	-0.0259	-0.218	0.0129	-0.1776	10.3261	29.3584	12.5464
13	8.2783	-3.205	0.702	1.6623	-1.1857	2.0415	-0.1024	0.0438	-0.1056	-0.0157	-0.1864	-0.1263	0.0363	-0.0568	0.2889	-0.1882	-0.0021	0.0115	-0.2044	-0.0252	-0.1433	28.7925	19.7986	19.4341
14	11.2046	-5.1874	-3.5258	4.8652	-1.0123	3.9485	-0.3579	-0.1234	0.1962	0.0087	0.5569	0.202	-0.0078	-0.0612	-0.1989	-0.1915	0.0265	0.0181	-0.1653	0.0264	-0.2409	11.4246	28.3961	26.8773
15	2.5428	-5.3648	4.3703	14.7368	-15.9648	33.6171	0.0361	0.0262	-0.5037	-0.6023	-0.6647	-0.6127	0.861	0.2302	0.6286	-0.3326	0.0495	0.0586	-0.1642	0.043	-0.1225	39.0242	23.663	10.5129
16	11.5025	10.5204	-14.3175	23.7015	-15.6928	18.3006	0.5151	0.0342	0.7041	1.2001	0.3921	0.3105	-0.7151	0.2176	-0.9072	-0.2465	0.0801	-0.017	-0.2442	0.0041	-0.1197	1.2544	36.3235	21.0482
17	23.4156	1.9986	-20.4731	7.1095	-6.1467	34.5192	0.13	-0.2103	0.921	0.4754	0.4015	-0.5697	-0.3718	0.15	-0.5315	-0.2556	-0.0035	-0.0803	-0.3301	-0.0186	-0.0933	36.9558	24.4952	23.8394
18	25.1871	-22.1434	15.3745	22.6738	-7.9374	19.0933	0.3194	1.4923	-0.0466	0.1963	-0.3621	0.1162	1.0935	0.71	0.0428	-0.2354	0.0493	0.0945	-0.1912	0.0739	-0.0503	3.0147	23.3853	23.6686
19	1.3221	0.0839	2.9198	2.3872	-3.2919	13.9527	-0.0947	0.03	-0.2955	0.0474	-0.0434	-0.4141	0.1801	-0.1208	0.1381	-0.2164	0.0197	0.0267	-0.2289	0.0215	-0.1219	35.769	22.1787	17.3752
20	3.9932	0.9994	-5.9002	10.5189	-7.5789	14.7268	0.064	-0.2669	-0.0271	-0.0119	0.0439	0.8841	-0.2635	0.0844	-0.1079	-0.3215	0.0447	-0.0082	-0.225	0.0625	-0.0984	4.0732	29.4188	24.6588
21	12.3021	-6.9532	-5.1575	12.4203	4.2655	15.5112	0.1515	0.5889	0.2296	-0.6573	-0.0135	0.0887	-0.3782	-0.2129	-0.138	-0.1913	0.0114	-0.0032	-0.1263	0.0299	-0.1313	19.0751	29.8422	12.8628

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	A	200

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi