PDB-8dxh: HIV-1 reverse transcriptase/rilpivirine with bound fragment 5-flu...

ID or keywords:

Entry

Database: PDB / ID: 8dxh

Title

HIV-1 reverse transcriptase/rilpivirine with bound fragment 5-fluoroquinazolin-4-ol at W266 site

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 type 1 group M subtype B

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 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	8dxh.cif.gz	481.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8dxh.ent.gz	346.8 KB	Display	PDB format
PDBx/mmJSON format	8dxh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8dxh_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	8dxh_full_validation.pdf.gz	1 MB	Display
Data in XML	8dxh_validation.xml.gz	44.6 KB	Display
Data in CIF	8dxh_validation.cif.gz	66.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dx/8dxh ftp://data.pdbj.org/pub/pdb/validation_reports/dx/8dxh	HTTPS FTP

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Related structure data

Related structure data	8dx2C 8dx3C 8dx8C 8dxbC 8dxeC 8dxgC 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)	161.999, 72.760, 109.393
Angle α, β, γ (deg.)	90.000, 100.589, 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 type 1 group M subtype B (isolate BH10) Strain: isolate BH10 / Gene: gag-pol / 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 type 1 group M subtype B (isolate BH10) 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 type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / 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 type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Production host:

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

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Non-polymers , 7 types, 724 molecules

#3: Chemical	ChemComp-JBQ / 5-fluoranyl-3,4-dihydroquinazolin-4-ol Mass: 166.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₇FN₂O / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 705 / 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: 2.78 Å³/Da / Density % sol: 55.74 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop 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: 1.8→50 Å / Num. obs: 115882 / % possible obs: 99.9 % / Redundancy: 3.6 % / R_merge(I) obs: 0.065 / R_pim(I) all: 0.039 / R_rim(I) all: 0.076 / Χ²: 1.014 / Net I/σ(I): 10.6 / Num. measured all: 413497

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
1.8-1.83	3.4	0.648	5756	0.677	0.397	0.763	0.928	99.9
1.83-1.86	3.6	0.521	5784	0.786	0.307	0.607	0.959	99.9
1.86-1.9	3.5	0.44	5725	0.82	0.262	0.514	1.015	99.9
1.9-1.94	3.5	0.37	5762	0.811	0.224	0.435	1.141	99.8
1.94-1.98	3.4	0.293	5798	0.88	0.18	0.345	1.035	99.9
1.98-2.03	3.5	0.243	5757	0.931	0.147	0.285	0.984	99.8
2.03-2.08	3.5	0.213	5748	0.906	0.128	0.25	1.057	99.9
2.08-2.13	3.5	0.169	5763	0.958	0.103	0.199	0.952	99.9
2.13-2.2	3.7	0.147	5800	0.973	0.086	0.171	0.918	99.9
2.2-2.27	3.6	0.136	5776	0.973	0.08	0.158	1.066	99.9
2.27-2.35	3.5	0.114	5792	0.978	0.069	0.134	0.996	99.9
2.35-2.44	3.5	0.1	5734	0.982	0.061	0.118	0.952	99.9
2.44-2.55	3.6	0.092	5796	0.985	0.056	0.108	1.008	99.9
2.55-2.69	3.6	0.083	5817	0.986	0.05	0.097	1.09	99.9
2.69-2.86	3.7	0.074	5775	0.99	0.044	0.087	0.967	100
2.86-3.08	3.6	0.069	5814	0.99	0.042	0.081	1.104	99.9
3.08-3.39	3.7	0.062	5841	0.992	0.037	0.072	1.055	99.9
3.39-3.88	3.8	0.054	5826	0.994	0.031	0.062	0.981	99.9
3.88-4.88	3.6	0.049	5844	0.995	0.029	0.057	1.058	99.9
4.88-50	3.6	0.047	5974	0.992	0.028	0.055	1.015	99.9

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Processing

Software

Name	Version	Classification
HKL-2000		data scaling
PHENIX	dev_3051	refinement
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4G1Q

4g1q

Resolution: 1.8→40.25 Å / SU ML: 0.2368 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.0699
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2129	3806	1.72 %
R_work	0.1897	216842	-
obs	0.1901	115872	96.64 %

Solvent computation

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

Displacement parameters

B_iso mean: 42.08 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→40.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7949	0	107	705	8761

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0149	8311
X-RAY DIFFRACTION	f_angle_d	1.3328	11292
X-RAY DIFFRACTION	f_chiral_restr	0.0802	1224
X-RAY DIFFRACTION	f_plane_restr	0.0097	1432
X-RAY DIFFRACTION	f_dihedral_angle_d	15.4684	3152

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 (%)
1.8-1.82	0.3984	129	0.3322	7409	X-RAY DIFFRACTION	89.1
1.82-1.84	0.3038	141	0.3055	7978	X-RAY DIFFRACTION	96.29
1.84-1.87	0.3493	139	0.2848	7977	X-RAY DIFFRACTION	96.14
1.87-1.9	0.3254	134	0.2633	8068	X-RAY DIFFRACTION	96.1
1.9-1.93	0.254	135	0.2474	7954	X-RAY DIFFRACTION	96.02
1.93-1.96	0.2542	145	0.2337	7959	X-RAY DIFFRACTION	95.78
1.96-1.99	0.2438	139	0.2247	7880	X-RAY DIFFRACTION	95.66
1.99-2.02	0.2132	144	0.2118	8138	X-RAY DIFFRACTION	96.27
2.02-2.06	0.2504	139	0.2152	7965	X-RAY DIFFRACTION	96.56
2.06-2.1	0.2333	135	0.2167	7868	X-RAY DIFFRACTION	95.74
2.1-2.14	0.2981	141	0.2164	8127	X-RAY DIFFRACTION	96.61
2.14-2.19	0.2412	145	0.2156	8058	X-RAY DIFFRACTION	96.99
2.19-2.24	0.2409	138	0.2017	7994	X-RAY DIFFRACTION	96.75
2.24-2.29	0.235	139	0.2	8018	X-RAY DIFFRACTION	96.51
2.29-2.36	0.2295	143	0.194	8031	X-RAY DIFFRACTION	96.56
2.36-2.43	0.193	141	0.2013	8072	X-RAY DIFFRACTION	96.51
2.43-2.5	0.2213	145	0.2027	8011	X-RAY DIFFRACTION	97.49
2.5-2.59	0.2395	140	0.1967	8074	X-RAY DIFFRACTION	96.77
2.59-2.7	0.259	143	0.2003	8153	X-RAY DIFFRACTION	97.7
2.7-2.82	0.2056	146	0.198	8079	X-RAY DIFFRACTION	97.68
2.82-2.97	0.1832	140	0.1928	8112	X-RAY DIFFRACTION	97.61
2.97-3.15	0.2164	146	0.199	8160	X-RAY DIFFRACTION	97.64
3.15-3.4	0.206	143	0.1879	8126	X-RAY DIFFRACTION	98.1
3.4-3.74	0.1982	143	0.174	8163	X-RAY DIFFRACTION	98.58
3.74-4.28	0.1592	141	0.1581	8153	X-RAY DIFFRACTION	97.54
4.28-5.39	0.1944	147	0.1562	8107	X-RAY DIFFRACTION	98.09
5.39-40.25	0.2049	145	0.1714	8208	X-RAY DIFFRACTION	98.4

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	0.147157137341	0.266508908291	0.107328470887	0.176627973483	0.217205872858	1.10559329776	0.122999698933	-0.0995237506264	-0.111672031986	0.12220041322	0.0681322198797	0.0244621017294	0.189599002445	0.00425385481179	0.0202800107718	0.315004975108	0.0157900475048	-0.0189730161358	0.252511675548	0.0351939753479	0.249877901467	47.4619003121	-21.6671819284	55.9783673329
2	0.746578289268	-0.465092764517	0.629462191356	0.295659582026	-0.314699986539	0.564205417833	0.0150635712023	-0.0862778029623	-0.140250922538	0.0423585086183	0.0931264069447	0.124969682654	0.0527834691308	-0.13788832568	0.000142945687053	0.172741696512	-0.00184200134809	0.0268653597142	0.216847602044	0.00691034011877	0.244485489818	23.5161203513	-5.82608602237	14.6764568116
3	0.459255078171	-0.103869041702	0.340472611048	0.624224237862	-0.250292583258	0.432371723243	-0.00960069793829	0.0116225372549	0.00289752233652	0.124686705347	-0.0693441412961	-0.00743114635628	-0.109701688928	0.171550256336	-3.21070687432E-5	0.255369490146	-0.0301539940806	-0.00280802178966	0.262658659074	0.00889179958441	0.214850381767	56.1160367138	1.42962714687	36.6826214284
4	0.0877120603162	-0.0259833355744	-0.0237758803443	0.031076673888	0.0261974800564	0.0143758483392	-0.149456764418	0.192515521174	0.265576603346	0.150574668961	-0.0301196260251	0.0912280967549	-0.0764481041302	0.0979430054953	-0.048692298694	0.591594407373	-0.138091431588	-0.14586251452	0.264418513062	0.137903627372	0.650736260251	55.633945156	25.9866250472	33.4944036704
5	0.970159329152	-0.51633625632	0.665315234781	0.843885994408	-0.188697866805	0.396088091184	-0.252824699303	0.468179454107	0.307498933453	0.281310835006	0.105107207293	-0.475091065231	-0.0175506655623	0.527536591185	0.0606514869252	0.205894325283	-0.275694840739	-0.083564095701	0.447092804874	0.127630208796	0.35541608036	64.4222502488	13.682571611	30.6755284778
6	0.0384225053413	0.017517143038	-0.061239591484	0.167889728671	-0.0700399486558	0.115217074709	-0.0939027155677	0.00303871226757	0.053601404964	0.0774028827243	-0.00698718852477	-0.153304767571	0.0389715961277	0.257600986483	2.2346409706E-7	0.216046330934	-0.0295494046791	0.0155028284921	0.299590136856	0.00939563661236	0.240125145587	30.7729451712	25.0365985859	2.84150617227
7	0.307797937458	0.347970110813	0.157231921391	0.703769913835	-0.0407449737678	0.808324046675	-0.114216710386	0.089224992073	0.186436659193	0.125426550403	-0.0143716195857	0.0374059458986	-0.181808477534	0.144388264746	3.62031943442E-8	0.245624968207	-0.0174258785723	-0.0105283080194	0.192722270705	-0.00921651171058	0.235670673792	33.3870519141	25.0253552183	9.3552320578
8	0.340290519387	-0.0795427360811	0.0759395298527	0.443654510814	-0.107215749652	0.286372869868	0.0136925277961	0.10474583826	0.0529615537011	0.0454217406139	-0.102799974417	0.00674336271546	-0.0361359967987	0.00914227403546	1.41144721101E-8	0.213571595365	-0.0182075361756	0.00630984742037	0.194077476223	-0.00372673324975	0.218451692633	43.1487870876	10.2566340235	20.1372140338

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid -1 through 253 )	A	A	-1 - 253	1 - 255
2	2	chain 'A' and (resid 254 through 554 )	A	A	254 - 554	256 - 556
3	3	chain 'B' and (resid 5 through 83 )	B	C	5 - 83	1 - 79
4	4	chain 'B' and (resid 84 through 104 )	B	C	84 - 104	80 - 100
5	5	chain 'B' and (resid 105 through 238 )	B	C	105 - 238	101 - 225
6	6	chain 'B' and (resid 239 through 269 )	B	C	239 - 269	226 - 256
7	7	chain 'B' and (resid 270 through 363 )	B	C	270 - 363	257 - 350
8	8	chain 'B' and (resid 364 through 428 )	B	C	364 - 428	351 - 415

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Related structure data

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Links

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Assembly

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Components

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Protein , 2 types, 2 molecules AB

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Non-polymers , 7 types, 724 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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