PDB-8dx2: HIV-1 reverse transcriptase/rilpivirine with bound fragment 4-ami...

ID or keywords:

Entry

Database: PDB / ID: 8dx2

Title

HIV-1 reverse transcriptase/rilpivirine with bound fragment 4-amino-3-bromopyridine at multiple sites

Components

Reverse transcriptase/ribonuclease H
p51 RT

Keywords

TRANSFERASE / HIV-1 reverse transcriptase

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

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Chopra, A. / Ruiz, F.X. / Bauman, J.D. / Arnold, E.

Funding support

United States, 1items

Citation

Journal: J.Med.Chem. / Year: 2023
Title: Halo Library, a Tool for Rapid Identification of Ligand Binding Sites on Proteins Using Crystallographic Fragment Screening.
Authors: Chopra, A. / Bauman, J.D. / Ruiz, F.X. / Arnold, E.

History

Deposition	Aug 2, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 31, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8dx2.cif.gz	478 KB	Display	PDBx/mmCIF format
PDB format	pdb8dx2.ent.gz	345.8 KB	Display	PDB format
PDBx/mmJSON format	8dx2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8dx2_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	8dx2_full_validation.pdf.gz	2.3 MB	Display
Data in XML	8dx2_validation.xml.gz	41.8 KB	Display
Data in CIF	8dx2_validation.cif.gz	59.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dx/8dx2 ftp://data.pdbj.org/pub/pdb/validation_reports/dx/8dx2	HTTPS FTP

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Related structure data

Related structure data	8dx3C 8dx8C 8dxbC 8dxeC 8dxgC 8dxhC 8dxiC 8dxjC 8dxkC 8dxlC 8dxmC 4g1qS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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	#33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #227 - Nov 2018 Telomerase similarity (1) #163 - Jul 2013 HIV Capsid similarity (1)

Deposited unit

A: Reverse transcriptase/ribonuclease H

B: p51 RT

hetero molecules

116 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)	161.918, 73.261, 109.247
Angle α, β, γ (deg.)	90.000, 100.379, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

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Protein , 2 types, 2 molecules AB

#1: Protein	Reverse transcriptase/ribonuclease H / Exoribonuclease H / p66 RT Mass: 63989.238 Da / Num. of mol.: 1 / Mutation: K172A, K173A, C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H
#2: Protein	p51 RT Mass: 50039.488 Da / Num. of mol.: 1 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03366

#1: Protein

Reverse transcriptase/ribonuclease H / Exoribonuclease H / p66 RT

Mass: 63989.238 Da / Num. of mol.: 1 / Mutation: K172A, K173A, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Human immunodeficiency virus 1 / Production host:

Escherichia coli (E. coli)
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H

#2: Protein

p51 RT

Mass: 50039.488 Da / Num. of mol.: 1 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Human immunodeficiency virus 1 / Strain: isolate BH10 / Gene: gag-pol / Production host:

Escherichia coli (E. coli) / References: UniProt: P03366

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Non-polymers , 7 types, 384 molecules

#3: Chemical	ChemComp-T27 / 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile / Rilpivirine Mass: 366.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₂H₁₈N₆ / Comment: medication, inhibitor*YM
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical	ChemComp-V06 / 3-bromopyridin-4-amine Mass: 173.011 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₅H₅BrN₂ / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.79 Å³/Da / Density % sol: 55.99 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10-12% PEG 8000, 4% PEG 400, 100 mM imidazole pH 6.4-6.6, 15 mM MgSO4, 100 mM amm sulfate, 5 mM TCEP PH range: 6.4-6.6

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 19, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. obs: 85019 / % possible obs: 98 % / Redundancy: 3.1 % / B_iso Wilson estimate: 37.54 Å² / R_merge(I) obs: 0.076 / R_pim(I) all: 0.051 / R_rim(I) all: 0.092 / Χ²: 1.08 / Net I/σ(I): 9.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2-2.03	2.9	0.578	3981	0.548	0.399	0.707	0.972	93.2
2.03-2.07	3.1	0.473	4198	0.666	0.323	0.576	1.034	98
2.07-2.11	2.9	0.368	4118	0.751	0.257	0.452	1.033	97.6
2.11-2.15	3.1	0.327	4206	0.807	0.222	0.397	1.113	98.2
2.15-2.2	3.1	0.291	4205	0.85	0.196	0.353	1.143	98.8
2.2-2.25	3.1	0.246	4161	0.872	0.167	0.299	1.175	98.5
2.25-2.31	3.1	0.215	4223	0.844	0.147	0.262	1.104	98.4
2.31-2.37	2.9	0.191	4171	0.921	0.134	0.235	1.151	98.2
2.37-2.44	3	0.17	4222	0.93	0.117	0.207	1.188	98.2
2.44-2.52	3.1	0.146	4149	0.942	0.1	0.178	1.137	97.9
2.52-2.61	3	0.126	4209	0.958	0.087	0.154	1.1	98
2.61-2.71	3.2	0.117	4182	0.962	0.078	0.142	1.053	98.2
2.71-2.84	3.1	0.106	4214	0.964	0.072	0.129	1.04	98.6
2.84-2.99	3.1	0.091	4231	0.973	0.062	0.111	1.081	98.6
2.99-3.17	3	0.084	4252	0.974	0.057	0.103	1.105	98.4
3.17-3.42	3	0.071	4200	0.98	0.048	0.087	0.985	98.4
3.42-3.76	3.2	0.065	4245	0.981	0.044	0.079	1.036	98.8
3.76-4.31	3.1	0.061	4249	0.982	0.041	0.074	1.006	98.3
4.31-5.43	3.1	0.056	4254	0.984	0.039	0.069	1.104	98.2
5.43-50	3.1	0.054	4349	0.987	0.036	0.065	1.04	98.1

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Processing

Software

Name	Version	Classification
PHENIX	dev_3051	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4G1Q

4g1q

Resolution: 2→38.05 Å / SU ML: 0.223 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8229 / Stereochemistry target values: GeoStd + Monomer Library

	R_factor	Num. reflection	% reflection
R_free	0.2434	3240	2.86 %
R_work	0.1883	110168	-
obs	0.1898	69545	67.7 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 56.12 Å²

Refinement step

Cycle: LAST / Resolution: 2→38.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7945	0	117	365	8427

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0091	8365
X-RAY DIFFRACTION	f_angle_d	0.9899	11379
X-RAY DIFFRACTION	f_chiral_restr	0.0585	1217
X-RAY DIFFRACTION	f_plane_restr	0.007	1432
X-RAY DIFFRACTION	f_dihedral_angle_d	20.6765	3155

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2-2.03	0.3212	129	0.2603	4426	X-RAY DIFFRACTION	62.04
2.03-2.06	0.318	138	0.247	4859	X-RAY DIFFRACTION	69.34
2.06-2.09	0.2727	135	0.2337	4818	X-RAY DIFFRACTION	67.9
2.09-2.13	0.2652	148	0.23	4876	X-RAY DIFFRACTION	69.11
2.13-2.17	0.2615	150	0.2169	4973	X-RAY DIFFRACTION	69.81
2.17-2.21	0.2486	158	0.2175	4878	X-RAY DIFFRACTION	69.5
2.21-2.25	0.2839	141	0.2075	4871	X-RAY DIFFRACTION	69.17
2.25-2.3	0.2521	146	0.2162	4843	X-RAY DIFFRACTION	68.07
2.3-2.36	0.2456	135	0.2029	4797	X-RAY DIFFRACTION	67.5
2.36-2.42	0.2199	141	0.2059	4743	X-RAY DIFFRACTION	67.76
2.42-2.48	0.2759	146	0.2086	4924	X-RAY DIFFRACTION	68.75
2.48-2.55	0.2569	138	0.2065	4679	X-RAY DIFFRACTION	67.16
2.55-2.64	0.2619	148	0.2063	4782	X-RAY DIFFRACTION	67.09
2.64-2.73	0.314	139	0.2113	4834	X-RAY DIFFRACTION	68.36
2.73-2.84	0.2978	134	0.2129	4816	X-RAY DIFFRACTION	68.26
2.84-2.97	0.259	136	0.2076	4836	X-RAY DIFFRACTION	68.34
2.97-3.13	0.2989	131	0.2187	4757	X-RAY DIFFRACTION	66.99
3.13-3.32	0.3091	143	0.2034	4793	X-RAY DIFFRACTION	67.37
3.32-3.58	0.2487	136	0.1944	4782	X-RAY DIFFRACTION	67.94
3.58-3.94	0.2185	148	0.1667	4769	X-RAY DIFFRACTION	67.87
3.94-4.51	0.1834	144	0.1507	4735	X-RAY DIFFRACTION	66.8
4.51-5.67	0.1893	137	0.1521	4716	X-RAY DIFFRACTION	66.53
5.67-38.05	0.2358	139	0.1724	4661	X-RAY DIFFRACTION	65.81

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	0.339294211457	0.301800723748	-0.0715992098474	0.127525585535	0.262903567397	0.208601766675	0.189835192998	-0.235184000131	-0.0448318035488	0.360605969312	-0.0871147090066	0.0861487976932	0.0902133928935	0.109039959088	0.0649656202724	0.598238608952	0.00817624281069	0.158224759026	0.381027224598	0.0312245306531	0.331494363868	46.7116479333	-15.5997092669	70.3827073597
2	-0.00759372534961	-0.0406555567817	0.268155052599	0.0196653635505	0.030575444522	0.171687195166	0.122568288949	0.0400750105762	-0.0267823712664	-0.0314735591506	0.0138142023865	0.104756193745	-0.0300325387329	-0.177757847137	0.00595704729676	0.493349274201	-0.0100643004682	0.0844788976074	0.334628554387	0.0548775537154	0.301203299806	39.8516195286	-17.4892834263	58.9004377825
3	0.173387269037	0.00689857960192	0.212580456405	-0.079558986987	0.0224302957948	0.215232840429	0.148372857441	-0.0915372462096	-0.11943320797	0.0594689992571	0.0764222809966	0.0810161824155	-0.00480642983955	0.0304108994489	0.103638894558	0.380471317817	0.0205695484643	0.0219806312749	0.291418117527	0.0323283063158	0.24316131109	51.9453365853	-20.320108629	54.7310679463
4	0.457534132372	0.473071288162	-0.0283607279843	0.430397210769	0.127305896357	0.598585116929	0.416190350148	-0.233868367956	-0.326861095148	0.314973938589	0.0587420917804	0.103785502579	0.227977130102	-0.333599319255	0.290575923811	0.355741023287	-0.0381168030628	0.00512544575419	0.298704205631	0.148860265282	0.416387240632	36.7845514625	-26.919749261	38.3800240748
5	0.0692012585887	-0.278548882179	0.301248404601	0.838655625531	-0.1814682301	0.364897042446	0.11224986891	-0.0169537647597	-0.187579700861	-0.0151454155399	0.0583178806837	0.235307654746	0.0420339953684	-0.160889332532	0.000310913406808	0.217112468012	0.00183364174551	-0.0276061204186	0.256709860914	-0.010612395089	0.33200851971	35.0877682868	-15.5942848914	17.4668678394
6	0.659591168213	-0.222590201248	0.949754065788	0.398225501486	-0.11551790133	0.386379884912	-0.0690892323203	-0.15413484121	-0.10643669232	0.0032207979221	0.134748994272	0.0552037336805	-0.0340592963277	-0.0456280956828	0.00581967069248	0.154525476063	0.0112940059706	0.0418672088123	0.349751167711	0.0141725826481	0.263774780301	13.0538941299	6.99468151694	6.66959621809
7	0.110500722503	0.172575002069	-0.0846113182756	0.0097464843845	0.0251902937408	0.00326890492211	0.0210702360093	0.0550432265578	0.0366294678922	-0.0717197982531	-0.198728448591	0.136898189294	-0.0835955624692	-0.00957843673713	6.42604722533E-7	0.222575951083	0.00628885845468	-0.00620143160951	0.282600214609	-0.0801352811932	0.371271521514	13.1315554793	17.5458168599	4.13704355625
8	0.570738858897	-0.132217325307	0.554001841973	0.990589891105	-0.26951643143	0.371171056013	-0.076640949957	0.10370227537	0.00573354885814	0.18948454425	-0.0923764880274	0.00153690394747	-0.127763099836	0.133755140585	-0.00111117306473	0.28942849962	-0.0347096396821	0.010580050577	0.245691881682	0.0249547194074	0.203357823482	56.4050151867	1.35023205952	36.7553342337
9	0.777666563214	-0.582104633099	1.07217532939	0.985186958235	-0.129197876561	0.319682881816	-0.299700311891	0.372348885235	0.386975983817	0.173681157097	-0.0465781443661	-0.425675372992	-0.0593611469842	0.383375392616	0.0438130813626	0.331961160151	-0.205455523712	-0.123165982117	0.354216259262	0.170661992026	0.453315731349	63.4529243615	15.5157450812	31.0670483299
10	0.141507511173	0.259025024348	0.103834368193	0.776516420546	-0.232742303517	0.947659566845	-0.11399124177	0.114362625431	0.101444603459	0.17274534712	0.0151400553753	0.0948170904133	-0.119880136689	0.0487593623082	-2.71101899359E-5	0.279377407877	-0.0222320723907	0.00486971938223	0.272367731728	-0.0257276200057	0.249582061776	32.8786122227	25.2711349747	7.88377178421
11	0.400786826252	-0.0841776158278	-0.00459649456321	0.559055740343	0.129551656382	0.360697911569	-0.0230559474559	0.286256494099	0.0612420676124	0.076583169106	-0.191051597455	0.0406236050712	-0.129237619624	0.0510086794316	-0.00102099034942	0.293438810646	-0.0286516488039	-0.00807605596182	0.265528097887	0.0146320107307	0.279284668705	43.0943557914	10.635800386	19.9547675367

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 58 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 59 through 96 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 97 through 194 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 195 through 296 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 297 through 421 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 422 through 527 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 528 through 554 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 5 through 83 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 84 through 238 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 239 through 363 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 364 through 428 )

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Protein , 2 types, 2 molecules AB

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Non-polymers , 7 types, 384 molecules

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Experiment

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-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

-
Protein , 2 types, 2 molecules AB

-
Non-polymers , 7 types, 384 molecules

-
Details

-
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