PDB-7lpw: Crystal Structure of HIV-1 RT in Complex with NBD-14189

ID or keywords:

Entry

Database: PDB / ID: 7lpw

Title

Crystal Structure of HIV-1 RT in Complex with NBD-14189

Components

(Reverse transcriptase ...) x 2

Keywords

TRANSFERASE/INHIBITOR / Human immunodeficiency virus 1 / non nucleotide-reverse transcriptase inhibitor / TRANSFERASE / TRANSFERASE-INHIBITOR complex

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

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.32 Å

Authors

Losada, N. / Ruiz, F.X. / Arnold, E.

Funding support

United States, 1items

Citation

Journal: J.Med.Chem. / Year: 2021
Title: HIV-1 gp120 Antagonists Also Inhibit HIV-1 Reverse Transcriptase by Bridging the NNRTI and NRTI Sites.
Authors: Losada, N. / Ruiz, F.X. / Curreli, F. / Gruber, K. / Pilch, A. / Das, K. / Debnath, A.K. / Arnold, E.

History

Deposition	Feb 12, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 17, 2021	Provider: repository / Type: Initial release
Revision 1.1	Dec 8, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Oct 18, 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	7lpw.cif.gz	469.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7lpw.ent.gz	344.2 KB	Display	PDB format
PDBx/mmJSON format	7lpw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7lpw_validation.pdf.gz	725 KB	Display	wwPDB validaton report
Full document	7lpw_full_validation.pdf.gz	756.5 KB	Display
Data in XML	7lpw_validation.xml.gz	39.8 KB	Display
Data in CIF	7lpw_validation.cif.gz	53.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lp/7lpw ftp://data.pdbj.org/pub/pdb/validation_reports/lp/7lpw	HTTPS FTP

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Related structure data

Related structure data	7lpxC 7lquC 4g1qS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6c0o-d 4ig3-d 5cyq-d 6c0n-d 4ify-d 4ifv-d 4idk-d 6c0p-d 6x4c-d 4i2p-d 6x47-d 6duf-d 7lqu-d 4kfb-d 5cym-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

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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) #163 - Jul 2013 HIV Capsid similarity (2) #227 - Nov 2018 Telomerase similarity (1)

Deposited unit

A: Reverse transcriptase p66

B: Reverse transcriptase p51

hetero molecules

115 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: 1 biological assembly in the asymmetric unit: A,B

Unit cell

Length a, b, c (Å)	161.433, 72.953, 107.747
Angle α, β, γ (deg.)	90.000, 99.874, 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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Reverse transcriptase ... , 2 types, 2 molecules AB

#1: Protein	Reverse transcriptase p66 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein	Reverse transcriptase p51 Mass: 50096.539 Da / Num. of mol.: 1 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03366

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Non-polymers , 5 types, 152 molecules

#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Chemical	ChemComp-YBA / ~{N}-[(1~{S})-2-azanyl-1-[4-(hydroxymethyl)-1,3-thiazol-2-yl]ethyl]-5-[3-fluoranyl-4-(trifluoromethyl)phenyl]-1~{H}-pyrrole-2-carboxamide Mass: 428.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₁₆F₄N₄O₂S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.84 Å³/Da / Density % sol: 56.68 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 10% PEG 8,000, 4% PEG 400, 100 mM imidazole pH 6.6,10 mM spermine, 15 mM MgSO4,100 mM (NH4)2SO4, and 5 mM tris(2-carboxyethyl)phosphine(TCEP)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.96868 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.96868 Å / Relative weight: 1
Reflection	Resolution: 2.316→34.82 Å / Num. obs: 53283 / % possible obs: 99.1 % / Redundancy: 5.9 % / B_iso Wilson estimate: 63.7 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.071 / R_pim(I) all: 0.03 / R_rim(I) all: 0.077 / Net I/σ(I): 23.6
Reflection shell	Resolution: 2.316→2.35 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.58 / Mean I/σ(I) obs: 2 / Num. unique obs: 2395 / CC_1/2: 0.49 / R_pim(I) all: 0.33 / R_rim(I) all: 0.67 / % possible all: 90.3

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4G1Q

4g1q

Resolution: 2.32→34.82 Å / SU ML: 0.3088 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.5654 / Stereochemistry target values: GeoStd + Monomer Library

	R_factor	Num. reflection	% reflection
R_free	0.2482	2000	3.76 %
R_work	0.2146	51253	-
obs	0.2159	53253	98.74 %

Solvent computation

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

Displacement parameters

B_iso mean: 92.28 Å²

Refinement step

Cycle: LAST / Resolution: 2.32→34.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7921	0	65	143	8129

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0058	8195
X-RAY DIFFRACTION	f_angle_d	0.8741	11139
X-RAY DIFFRACTION	f_chiral_restr	0.1611	1203
X-RAY DIFFRACTION	f_plane_restr	0.0051	1397
X-RAY DIFFRACTION	f_dihedral_angle_d	19.972	3088

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 (%)
2.32-2.37	0.3624	125	0.3192	3213	X-RAY DIFFRACTION	87.27
2.37-2.44	0.3271	141	0.2997	3604	X-RAY DIFFRACTION	98.17
2.44-2.51	0.3381	142	0.2835	3653	X-RAY DIFFRACTION	98.85
2.51-2.59	0.3045	143	0.2665	3669	X-RAY DIFFRACTION	99.56
2.59-2.68	0.2872	144	0.2635	3679	X-RAY DIFFRACTION	99.58
2.68-2.79	0.3051	144	0.2584	3680	X-RAY DIFFRACTION	99.77
2.79-2.92	0.2775	144	0.2453	3689	X-RAY DIFFRACTION	99.87
2.92-3.07	0.2954	143	0.251	3685	X-RAY DIFFRACTION	99.95
3.07-3.26	0.2892	145	0.2541	3703	X-RAY DIFFRACTION	99.92
3.26-3.52	0.2794	144	0.2357	3686	X-RAY DIFFRACTION	99.9
3.52-3.87	0.2824	145	0.2194	3729	X-RAY DIFFRACTION	99.97
3.87-4.43	0.2066	145	0.1881	3721	X-RAY DIFFRACTION	100
4.43-5.57	0.2176	146	0.1875	3735	X-RAY DIFFRACTION	99.97
5.57-34.82	0.2132	149	0.1889	3807	X-RAY DIFFRACTION	99.52

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	4.88524103889	1.99607612188	-3.37890982733	2.14448574459	-0.340290131761	3.94814135732	0.424200002951	-0.203099494293	-0.0578065684205	0.537337029445	-0.224703484464	0.432304626314	0.0811525628273	0.153104405478	-0.246109258049	1.11115029214	-0.00985076383201	0.0931036787205	0.63135730868	0.0466137870148	0.599373088927	209.257773441	-13.9110292031	69.7319285954
2	0.548715258796	0.322869940237	-1.0277980339	1.91255016753	3.10110704799	6.96396392942	0.382060656039	0.0335123930682	0.239752951646	0.424115034055	-0.025395292197	0.190332617493	0.11606502268	-1.05245155426	-0.329213873334	0.829271147452	0.0269369378227	-0.00737500473369	0.852044746874	0.187462241259	0.672799273594	202.441967822	-15.687977806	57.9770129719
3	0.0639754543494	0.653828928981	0.431306707205	0.234301261069	-0.35552376871	2.24176048556	0.126936538938	-0.174471626828	-0.256059638289	0.211466156769	0.163017946763	0.382763228147	0.0980192611172	-0.603741955185	-0.322091387628	0.873682159071	0.00955650713123	-0.0670702333323	0.709289609163	0.146906402447	0.922249756499	205.529409337	-21.9223729242	45.6464958282
4	2.78372662768	-1.30168247864	1.37781230052	2.61888528064	-1.51838020943	3.32757921876	0.135353953382	-0.276533034799	-0.560065965726	0.0680629003418	0.237826707501	0.358611560087	0.289261680477	-0.317401560682	-0.328682338993	0.563405814568	-0.0346770970627	-0.055957409051	0.429409409628	-0.0109118770152	0.59194757976	197.037294995	-14.4364115982	17.4690084902
5	5.81072509891	-1.88240964693	0.359377138253	2.67416710316	-0.208428212701	1.13635290047	-0.0629422187654	-0.282541944669	-0.0542801370431	0.12809352096	0.238044480724	0.129554785262	0.0713470586763	-0.161620741283	-0.169045975523	0.420703510678	-0.0365042075841	0.0187628004591	0.486909874691	0.0178416245287	0.421820612404	172.808601154	9.82345014955	5.06415635684
6	4.30127605013	2.33233110585	-0.193108285162	6.76150163024	0.334198796378	6.67513862665	0.0183319394593	-0.280629502316	0.0962746410705	-0.0194575356311	-0.0381463824495	0.570163309899	-0.367722685301	-0.441893917095	-0.0591919386589	0.306373103261	0.0570044526956	-0.0359126914392	0.532010517224	0.0183394896871	0.460679517435	176.720747018	10.063864266	7.5050582618
7	6.31526838944	-0.783995358903	1.06582983058	6.75748987998	1.55140424827	4.05204945532	-0.128956289262	-0.110743146872	0.0983904865091	0.581150006758	-0.0139057094984	-0.240882565542	-0.154730682708	0.342712347499	0.0873233175229	0.643359742139	-0.0578412891537	-0.0777338807161	0.405956172785	0.118325863841	0.313455544787	218.182345593	3.10691368993	36.2077075001
8	2.15968718086	0.529290770601	-0.105695899567	5.76137004312	-1.76200316803	2.71423499188	-0.0838198910068	0.144261206748	0.630267603978	0.6298385691	0.0137255892089	-0.376220485743	-0.626060402671	0.406181314965	0.0741114721293	0.797249920385	-0.1667209454	-0.181986202264	0.625415653232	0.0522255704436	0.712481867968	222.388518688	17.0975493523	33.5833861114
9	8.31279223792	-0.719542849544	5.12583763403	-0.331161605066	0.30212838415	3.82051263769	-0.068841223499	0.492131871874	-0.164117965637	0.12734898078	0.178157264124	-0.185175901502	-0.0634491367242	0.545259567871	-0.11585073067	0.599605597269	-0.110225656956	-0.0655611328977	0.660214113002	0.0845464911811	0.72936912216	212.540103654	23.7277324452	11.5048231055
10	2.88478426157	0.203843119314	2.59994188022	3.76990364346	-0.46841283523	3.62172154845	-0.319981397322	-0.118982255027	0.531130383643	0.414623459627	-0.115647705225	-0.210013048087	-0.443845891808	-0.0869946452161	0.503022857565	0.569763599297	-0.0252912452839	0.111693544116	0.462167398981	0.0395891360407	0.414306288513	194.444138917	26.0422823332	8.98476387768
11	5.54985120726	-1.49210636757	2.2446084748	8.28849646327	0.0691030158896	1.63423397418	0.138680962265	0.237320307973	0.184002381916	0.172321988622	-0.326567804645	-0.138117950478	-0.00524671793162	0.0575213925647	0.220390653156	0.528754502832	-0.0522548776314	0.0604485120391	0.467561228803	0.0492288425896	0.357292646035	204.53636008	11.6074802478	20.0853809132

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 59 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 60 through 96 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 97 through 298 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 299 through 421 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 422 through 499 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 500 through 554 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 5 through 83 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 84 through 194 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 195 through 269 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 270 through 363 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 364 through 428 )

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