PDB-2q55: Crystal structure of KK44 bound to HIV-1 protease

ID or keywords:

Entry

Database: PDB / ID: 2q55

Title

Crystal structure of KK44 bound to HIV-1 protease

Components

Protease

Keywords

HYDROLASE / Drug design / HIV-1 protease / protease inhibitor

Function / homology

Function and homology information

RNA-directed DNA polymerase activity / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function

Biological species

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

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

Citation

Journal: J.Med.Chem. / Year: 2007
Title: Design and Synthesis of HIV-1 Protease Inhibitors Incorporating Oxazolidinones as P2/P2' Ligands in Pseudosymmetric Dipeptide Isosteres.
Authors: Reddy, G.S. / Ali, A. / Nalam, M.N. / Anjum, S.G. / Cao, H. / Nathans, R.S. / Schiffer, C.A. / Rana, T.M.

History

Deposition	May 31, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 4, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Derived calculations / Version format compliance
Revision 1.2	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.3	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 1.4	Aug 30, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5	Mar 13, 2024	Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2q55.cif.gz	56.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2q55.ent.gz	42.2 KB	Display	PDB format
PDBx/mmJSON format	2q55.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2q55_validation.pdf.gz	744.6 KB	Display	wwPDB validaton report
Full document	2q55_full_validation.pdf.gz	744.5 KB	Display
Data in XML	2q55_validation.xml.gz	10.9 KB	Display
Data in CIF	2q55_validation.cif.gz	15.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q5/2q55 ftp://data.pdbj.org/pub/pdb/validation_reports/q5/2q55	HTTPS FTP

-
Related structure data

Related structure data	2q54C 2q5kC 1f7aS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3o9e-d 3o9a-d 2uxz-d 3sa6-d 3sa5-d 6w6t-d 6dh6-d 6opx-d 4hla-d 4dqg-d 5tyr-d 2bpx-d 3sac-d 3s54-d 4rvx-1 6dh4-d 4rvi-2 4j54-d 3o9h-d 2qi0-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

22.5 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)	50.844, 58.530, 61.869
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: O38719*PLUS
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄ Details: Synthesized in the laboratory to inhibit the HIV-1 protease
#3: Chemical	ChemComp-MU0 / (5S)-N-[(1S,2S,4S)-1-BENZYL-2-HYDROXY-4-{[(2S)-3-METHYL-2-(2-OXOTETRAHYDROPYRIMIDIN-1(2H)-YL)BUTANOYL]AMINO}-5-PHENYLPENTYL]-2-OXO-3-PHENYL-1,3-OXAZOLIDINE-5-CARBOXAMIDE Mass: 655.783 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₇H₄₅N₅O₆
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.13 Å³/Da / Density % sol: 42.16 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 126 mM sodium phosphate, 63 mM sodium citrate, 24-29%% ammonium sulphate, pH 6.2, 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: Aug 24, 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: 1.9→50 Å / Num. obs: 15088 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / R_merge(I) obs: 0.054 / R_sym value: 5.4 / Net I/σ(I): 10.1

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
HKL-2000		data reduction
HKL-2000		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 1F7A

1f7a

Resolution: 1.9→42.52 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.916 / SU B: 6.46 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.161 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23473	757	5 %	RANDOM
R_work	0.17481	-	-	-
obs	0.17763	14290	99.47 %	-

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: 17.713 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.53 Å²	0 Å²	0 Å²
2-	-	0.02 Å²	0 Å²
3-	-	-	0.51 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→42.52 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1498	0	58	136	1692

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	1594
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1537
X-RAY DIFFRACTION	r_angle_refined_deg	1.292	2.025	2172
X-RAY DIFFRACTION	r_angle_other_deg	0.697	3	3567
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.314	5	198
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.652	24.815	54
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.886	15	265
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.199	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	257
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1732
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	291
X-RAY DIFFRACTION	r_nbd_refined	0.174	0.2	228
X-RAY DIFFRACTION	r_nbd_other	0.176	0.2	1512
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	741
X-RAY DIFFRACTION	r_nbtor_other	0.079	0.2	969
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	106
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	0.112	0.2	10
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.18	0.2	44
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.11	0.2	9
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	0.51	1.5	1047
X-RAY DIFFRACTION	r_mcbond_other	0.113	1.5	414
X-RAY DIFFRACTION	r_mcangle_it	0.741	2	1599
X-RAY DIFFRACTION	r_scbond_it	1.211	3	660
X-RAY DIFFRACTION	r_scangle_it	1.782	4.5	573
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→1.948 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.282	51	-
R_work	0.215	982	-
obs	-	-	93.65 %

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	2.5607	-2.2486	-0.1752	2.7395	-0.0777	4.927	-0.113	-0.071	-0.2466	0.1188	0.1136	0.2748	0.1093	-0.1086	-0.0007	-0.0433	0.0077	0.0245	-0.0779	0.0175	-0.0333	19.7117	17.8628	23.1344
2	4.4611	-0.8246	0.6914	7.3419	1.3477	1.6279	-0.1082	-0.2888	0.1241	0.1438	0.0546	-0.0079	0.0332	0.0434	0.0536	-0.0113	0.0403	0.011	-0.0151	-0.0054	-0.1344	21.0471	25.9846	29.195
3	7.9361	-0.3911	1.3051	3.4909	0.4455	1.1645	0.1157	-0.0047	-0.1476	-0.1272	-0.0836	-0.0144	-0.0749	-0.1077	-0.0322	-0.0415	0.0108	0.0121	-0.0452	-0.0247	-0.0573	12.7912	26.8004	18.332
4	5.7084	2.8357	1.4431	3.8347	0.8908	1.9574	-0.1187	-0.0194	0.02	-0.1174	0.0022	-0.0367	-0.1312	0.006	0.1166	-0.0361	0.02	-0.005	-0.0563	0.0107	-0.057	27.7507	28.4587	19.072
5	27.9493	-12.7228	1.8182	7.4705	-2.3817	2.7217	-0.0492	0.1676	-0.6788	0.0891	0.0443	0.3498	-0.0178	-0.1646	0.0049	-0.0748	-0.0349	0.0151	-0.0189	-0.042	0.0131	1.6286	21.5587	17.9153
6	13.5855	-4.2948	-0.8149	3.3679	3.508	5.3048	-0.0323	-0.2308	-0.0653	0.2565	-0.0092	-0.47	0.027	0.3754	0.0416	-0.0191	-0.0254	-0.0447	-0.0719	0.0314	0.0042	39.0026	30.6838	24.1981
7	11.6694	1.0581	-3.6621	9.0463	3.2589	4.6192	-0.0726	0.475	-0.014	-0.0122	0.0457	0.4335	0.2259	-0.409	0.0269	-0.0647	0.0132	-0.051	0.0078	0.0754	-0.1073	0.485	34.1024	13.4858
8	6.7792	1.0607	-0.3699	2.7071	3.1621	7.1576	0.0699	0.0617	0.116	0.0178	0.0795	-0.4083	-0.1537	0.3523	-0.1494	-0.0352	-0.0026	-0.0283	-0.0734	0.0545	-0.0292	39.5751	31.4174	10.5497
9	16.6592	-3.2348	-2.7164	3.4587	-1.9145	2.5496	0.0604	0.1321	0.0378	-0.0019	-0.0254	0.1332	0.0154	0.0075	-0.035	-0.011	0.0102	0.0064	-0.0616	-0.003	-0.0531	12.714	39.4139	11.2061
10	15.7957	-3.8463	-2.0909	3.5837	0.3646	3.1539	0.1429	0.1241	-0.1042	0.0176	-0.0177	0.0133	-0.1389	0.0743	-0.1251	-0.0244	-0.007	0.0014	-0.0797	-0.0045	-0.0962	27.4623	30.9908	4.6017
11	4.374	-6.6774	5.8248	12.3729	-8.4683	7.8392	0.4394	0.2434	0.0551	-0.5483	-0.2669	0.1936	0.4295	0.2607	-0.1725	-0.052	0.0164	-0.033	-0.0117	0.0058	-0.0299	10.585	29.3009	12.4565
12	1.946	-0.5377	0.2525	5.8283	-0.4992	2.1675	0.0632	0.0484	0.2001	0.0471	0.0769	0.5024	-0.2516	0.1164	-0.1401	-0.0462	-0.0047	-0.0147	-0.0352	0.011	-0.0249	29.4839	33.1426	14.7288
13	4.4377	-1.9195	-1.7865	3.9924	-0.3358	1.1077	-0.0478	-0.4603	0.0691	0.0207	0.0577	0.3152	0.0001	0.0391	-0.0099	-0.0176	0.0418	-0.0004	0.0346	0.002	-0.045	11.6605	28.6662	26.8494
14	6.0806	1.3047	1.2217	2.8572	0.9641	0.4741	-0.0167	0.0724	-0.1658	-0.0945	0.0606	-0.1585	-0.0913	-0.0253	-0.0439	-0.0239	0.0074	0.0117	-0.0475	-0.0064	-0.0159	29.045	19.8138	19.8033
15	11.022	7.7816	-12.9655	11.5382	-12.5856	17.2004	0.402	-0.1989	0.5151	0.3351	0.0479	0.294	-0.3175	0.2778	-0.4499	-0.0794	0.0343	0.0027	-0.052	0.0007	0.0491	1.4272	36.276	20.8287
16	4.1949	-8.1441	7.246	16.7001	-10.5564	26.3878	-0.0395	0.3491	-0.6318	-0.5703	-0.0107	-0.2931	0.3772	0.6118	0.0502	-0.1491	0.0042	0.0786	0.0429	0.0314	-0.001	39.173	23.5989	10.7375
17	17.2637	-16.5893	0.8441	21.527	-2.6719	8.4596	0.0268	0.6566	-0.0699	-0.4705	-0.2012	0.0689	0.567	0.395	0.1744	-0.0322	0.0371	0.0203	-0.0168	-0.0004	-0.052	3.1553	23.4255	23.85
18	15.4847	-0.6758	-9.9828	11.983	1.7013	42.0496	0.3442	-0.3042	0.697	0.2994	0.307	-0.0817	-0.0831	-0.2854	-0.6512	-0.1109	-0.0199	-0.0719	-0.187	0.003	0.0067	37.0917	24.5866	24.1317
19	3.4173	-0.6846	-3.7144	4.9472	-3.4669	8.5847	0.082	-0.1953	0.0604	-0.1538	0.0991	0.4018	-0.0161	0.0939	-0.1811	-0.1018	0.0071	-0.0473	-0.0524	-0.0078	-0.022	4.2483	29.5363	24.628
20	4.2208	-0.4342	0.8431	3.7011	-0.2716	3.9522	-0.0609	0.0046	-0.2486	-0.0347	-0.0415	-0.2725	0.0788	0.2735	0.1024	-0.0936	-0.0015	0.0163	-0.0558	0.0183	-0.0134	36.4198	21.9699	18.3714
21	13.176	2.3632	-3.8485	5.7554	3.8745	14.4484	-0.0361	0.0526	0.2086	-0.0889	0.1463	0.1043	-0.4833	-0.3493	-0.1102	-0.0081	0.037	0.0065	-0.049	0.0639	-0.1268	19.9673	30.58	13.5153

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 5	1 - 5
2	X-RAY DIFFRACTION	1	A	A	94 - 99	94 - 99
3	X-RAY DIFFRACTION	1	A	A	6 - 10	6 - 10
4	X-RAY DIFFRACTION	2	B	B	1 - 5	1 - 5
5	X-RAY DIFFRACTION	2	B	B	94 - 99	94 - 99
6	X-RAY DIFFRACTION	2	B	B	6 - 10	6 - 10
7	X-RAY DIFFRACTION	3	A	A	20 - 32	20 - 32
8	X-RAY DIFFRACTION	4	B	B	20 - 32	20 - 32
9	X-RAY DIFFRACTION	5	A	A	11 - 20	11 - 20
10	X-RAY DIFFRACTION	6	B	B	11 - 20	11 - 20
11	X-RAY DIFFRACTION	7	A	A	33 - 43	33 - 43
12	X-RAY DIFFRACTION	8	B	B	33 - 43	33 - 43
13	X-RAY DIFFRACTION	9	A	A	44 - 57	44 - 57
14	X-RAY DIFFRACTION	10	B	B	44 - 57	44 - 57
15	X-RAY DIFFRACTION	11	A	A	77 - 85	77 - 85
16	X-RAY DIFFRACTION	12	B	B	77 - 85	77 - 85
17	X-RAY DIFFRACTION	13	A	A	86 - 93	86 - 93
18	X-RAY DIFFRACTION	14	B	B	86 - 93	86 - 93
19	X-RAY DIFFRACTION	15	A	A	57 - 62	57 - 62
20	X-RAY DIFFRACTION	16	B	B	57 - 62	57 - 62
21	X-RAY DIFFRACTION	17	A	A	63 - 68	63 - 68
22	X-RAY DIFFRACTION	18	B	B	63 - 68	63 - 68
23	X-RAY DIFFRACTION	19	A	A	69 - 76	69 - 76
24	X-RAY DIFFRACTION	20	B	B	69 - 76	69 - 76
25	X-RAY DIFFRACTION	21	B	E	200	1

-
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