PDB-2i0a: Crystal Structure of KB-19 complexed with wild type HIV-1 protease

ID or keywords:

Entry

Database: PDB / ID: 2i0a

Title

Crystal Structure of KB-19 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: 1.8 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	2i0a.cif.gz	59.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2i0a.ent.gz	43.8 KB	Display	PDB format
PDBx/mmJSON format	2i0a.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2i0a_validation.pdf.gz	729.8 KB	Display	wwPDB validaton report
Full document	2i0a_full_validation.pdf.gz	730.7 KB	Display
Data in XML	2i0a_validation.xml.gz	11.9 KB	Display
Data in CIF	2i0a_validation.cif.gz	16.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i0/2i0a ftp://data.pdbj.org/pub/pdb/validation_reports/i0/2i0a	HTTPS FTP

-
Related structure data

Related structure data	2i0dC 1f7aS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4njt-1 6pjl-d 1hvc-d 6pu8-d 2qhy-d 4a4q-d 3st5-d 1mer-d 1npv-d 1t3r-d 2qi6-d 5w5w-d 3gi6-d 4djr-d 2aid-d 4f73-d 7hvp-d 6d0e-d 1g2k-d 1kzk-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)	50.769, 57.656, 61.892
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: O38723*PLUS
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-MUI / (5S)-3-(4-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-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.: 173 / 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: 2.09 Å³/Da / Density % sol: 41.22 %
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: Nov 30, 2005 / 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: 1.7→50 Å / Num. obs: 17942 / % possible obs: 86.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / R_merge(I) obs: 0.05 / R_sym value: 0.05 / Net I/σ(I): 14.4

-
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: 1.8→42.18 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.947 / SU B: 4.243 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.134 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18506	854	5.1 %	RANDOM
R_work	0.15975	-	-	-
obs	0.16103	15778	95.61 %	-
all	-	15778	-	-

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: 13.72 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.59 Å²	0 Å²	0 Å²
2-	-	0.01 Å²	0 Å²
3-	-	-	0.58 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→42.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1494	0	71	173	1738

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	1624
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1544
X-RAY DIFFRACTION	r_angle_refined_deg	1.232	2.029	2219
X-RAY DIFFRACTION	r_angle_other_deg	0.686	3	3584
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.854	5	204
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.084	24.909	55
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.268	15	267
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.299	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	258
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1764
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	289
X-RAY DIFFRACTION	r_nbd_refined	0.178	0.2	215
X-RAY DIFFRACTION	r_nbd_other	0.171	0.2	1546
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	749
X-RAY DIFFRACTION	r_nbtor_other	0.08	0.2	982
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.131	0.2	128
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.127	0.2	13
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.187	0.2	77
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.116	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	0.448	1.5	1066
X-RAY DIFFRACTION	r_mcbond_other	0.088	1.5	420
X-RAY DIFFRACTION	r_mcangle_it	0.664	2	1630
X-RAY DIFFRACTION	r_scbond_it	1.031	3	677
X-RAY DIFFRACTION	r_scangle_it	1.533	4.5	589

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.189	44	-
R_work	0.17	773	-
obs	-	-	65.99 %

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	3.4721	-0.5939	-0.7118	3.2864	0.9966	1.952	-0.0573	-0.1246	0.0678	0.238	-0.0184	-0.03	0.0021	0.0079	0.0757	-0.0119	0.0239	-0.0005	-0.0304	0.0039	-0.1034	21.0922	25.6622	29.3648
2	2.9072	-1.2617	0.4912	1.9672	0.1054	3.1605	-0.055	0.0458	-0.2175	0.1147	0.1065	0.1865	0.1546	-0.0018	-0.0515	-0.0288	-0.0041	0.0225	-0.0775	0.0223	-0.0314	19.6705	17.5259	23.2566
3	2.4279	0.78	0.5969	2.6311	-0.7267	0.5011	-0.0131	-0.0017	-0.0241	0.0362	-0.0653	-0.0645	-0.0535	-0.0172	0.0785	-0.0268	0.0007	-0.0075	-0.0311	0.0096	-0.0415	27.6512	28.1272	19.0281
4	4.2879	1.2648	1.2579	4.5978	0.8167	1.944	0.029	0.0272	-0.0574	-0.1208	0.0192	0.102	-0.0207	0.0128	-0.0482	-0.0252	0.0052	0.0127	-0.0482	0.0101	-0.0468	12.6968	26.574	18.6709
5	4.3918	0.5045	-2.0826	5.2494	-1.7582	7.9297	-0.1103	-0.2968	-0.1658	0.147	-0.2604	-0.7642	0.0149	0.4551	0.3707	-0.0572	-0.0171	-0.0684	-0.0573	0.0762	0.0524	39.0182	30.278	23.9339
6	17.6827	-4.55	-0.2406	5.9389	1.4827	9.417	0.1398	-0.0525	-0.5773	-0.0534	0.009	0.7329	-0.2211	-0.8142	-0.1489	-0.0643	-0.0122	0.0089	0.0044	0.0191	0.0656	1.6767	21.4102	18.3083
7	4.4632	0.3076	1.8492	2.6673	1.741	2.3489	0.0327	0.0807	-0.0019	-0.085	0.069	-0.1286	-0.186	0.329	-0.1017	-0.0455	-0.0222	0.0206	-0.0275	0.0357	-0.0282	39.5407	31.0092	10.5317
8	6.8805	-0.6538	-0.3571	4.1663	1.7539	3.0922	0.1429	0.1371	-0.0926	-0.0741	-0.064	0.2386	0.1816	-0.2798	-0.0789	-0.0623	-0.0011	-0.0071	0.0029	0.0656	-0.058	0.3758	33.9471	13.7418
9	11.1111	-0.862	-2.6129	0.5891	-0.445	2.4125	0.0364	0.0283	0.0483	-0.0656	-0.0527	-0.0109	-0.1206	0.0145	0.0164	-0.0122	0.0016	0.0025	-0.0441	-0.0135	-0.0388	27.3053	30.6996	4.6155
10	6.3803	-2.0756	-2.5612	2.7497	0.1633	1.2444	0.1507	0.0824	0.214	-0.1346	-0.0006	0.0859	-0.0533	-0.032	-0.1501	-0.0161	0.0027	-0.0092	-0.0313	0.0104	-0.0287	12.7316	38.918	11.4829
11	1.2003	-0.626	-0.6454	2.7556	-0.6196	2.2305	-0.0203	-0.0152	0.0529	0.0625	0.0212	0.0988	-0.2311	-0.0381	-0.0009	-0.0271	-0.0086	-0.0119	-0.0257	0.0058	-0.0226	29.2249	32.6418	14.7176
12	1.9537	-2.089	2.2445	3.2082	-1.6624	3.4208	0.169	0.1444	-0.0182	-0.121	-0.0292	0.0471	0.1727	0.0769	-0.1397	-0.0234	0.0028	-0.0059	-0.0242	0.0131	-0.0152	10.3752	29.0736	12.762
13	2.5055	0.4116	-0.5086	2.3679	-0.761	0.3028	-0.0413	0.0819	-0.1051	0.0317	0.0028	-0.0577	-0.0126	0.1092	0.0385	0.0018	0.0083	0.002	-0.0189	-0.0005	-0.0059	28.9133	19.5069	19.696
14	1.0086	-1.3825	-0.0276	1.9887	0.1154	3.0428	-0.2378	-0.2053	0.13	-0.0237	0.2616	0.2371	0.0554	-0.024	-0.0238	-0.0193	0.0324	0.0251	-0.0024	0.0132	-0.02	11.7173	28.4012	27.1052
15	0.1757	-1.5956	1.4477	14.5738	-12.4153	18.0743	0.1259	0.0611	-0.4065	-0.4879	-0.5005	-0.4219	0.27	0.6234	0.3746	-0.1136	0.0553	0.0715	0.009	0.053	0.0081	39.1377	23.0729	10.5991
16	5.0372	6.9931	-5.135	10.3314	-9.4211	13.6719	0.3547	-0.2054	0.4596	0.4782	0.1507	0.5132	-0.47	-0.0135	-0.5053	-0.0836	0.0575	0.0201	-0.047	0.0441	0.0687	1.4422	36.2185	21.2457
17	10.1899	-1.2205	-7.8198	7.3963	-0.5699	14.2859	0.0615	0.1407	0.744	0.3597	-0.0005	-0.3054	-0.1124	-0.0074	-0.061	-0.0941	-0.025	-0.0848	-0.0855	0.0507	0.0149	37.0801	24.2218	23.8817
18	20.192	-14.5081	5.8549	20.9582	-0.6642	8.1301	0.0795	0.724	0.0079	0.2114	-0.35	-0.0775	0.4593	0.3646	0.2705	-0.0629	0.0292	0.0428	-0.0373	0.0495	-0.0227	3.3739	23.1265	24.3212
19	0.9203	0.8242	-1.5115	2.3749	-0.0146	3.5778	-0.0093	-0.0071	-0.127	0.0123	-0.0846	-0.1896	0.0799	0.3044	0.0938	-0.0634	0.0055	0.0144	-0.0172	0.0208	0.0007	36.3444	21.5844	18.2691
20	1.9937	2.1748	-3.9727	6.1748	-4.6488	7.9423	0.082	-0.1129	0.1252	-0.0326	0.0825	0.4876	0.0291	0.184	-0.1645	-0.0668	0.0236	-0.0116	-0.0274	0.0327	0.0139	4.2103	29.3369	24.9547
21	3.7558	-0.3891	-0.6579	3.7522	-1.0151	2.281	-0.0368	-0.1376	-0.097	-0.1523	0.1108	0.1095	-0.1274	0.0339	-0.0741	0.0136	0.0072	-0.0058	0.003	0.0022	-0.0205	19.3576	29.3706	12.9475

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://pdbjlvh1.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