PDB-4kfb: HIV-1 reverse transcriptase with bound fragment at NNRTI adjacent site

ID or keywords:

Entry

Database: PDB / ID: 4kfb

Title

HIV-1 reverse transcriptase with bound fragment at NNRTI adjacent site

Components

P51 RT
REVERSE TRANSCRIPTASE/RIBONUCLEASE H, EXORIBONUCLEA P66 RT

Keywords

transferase/transferase inhibitor / RNA-DIRECTED DNA POLYMERASE / DNA POLYMERASE / ENDONUCLEASE / HYDROLASE / MULTIFUNCTIONAL ENZYME / HYDROLASE-INHIBITOR COMPLEX / 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 / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...
Similarity search - Function

HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...
Similarity search - Domain/homology

Biological species

HUMAN IMMUNODEFICIENCY VIRUS TYPE 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.854 Å

Authors

Bauman, J.D. / Patel, D. / Arnold, E.

Citation

Journal: J.Med.Chem. / Year: 2013
Title: Detecting Allosteric Sites of HIV-1 Reverse Transcriptase by X-Ray Crystallographic Fragment Screening.
Authors: Bauman, J.D. / Patel, D. / Dharia, C. / Fromer, M.W. / Ahmed, S. / Frenkel, Y. / Vijayan, R.S. / Eck, J.T. / Ho, W.C. / Das, K. / Shatkin, A.J. / Arnold, E.

History

Deposition	Apr 26, 2013	Deposition site: RCSB / Processing site: RCSB
Supersession	May 15, 2013	ID: 4I7G
Revision 1.0	May 15, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jun 17, 2015	Group: Non-polymer description
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4kfb.cif.gz	428.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4kfb.ent.gz	349.1 KB	Display	PDB format
PDBx/mmJSON format	4kfb.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kf/4kfb ftp://data.pdbj.org/pub/pdb/validation_reports/kf/4kfb	HTTPS FTP

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Related structure data

Related structure data	4iclC 4id5C 4idkC 4ifvC 4ifyC 4ig0C 4ig3C C: citing same article (ref.)
Similar structure data	4g1q-d 6x4c-d 6eli-d 2zd1-d 4i2p-d 4ig3-d 4icl-d 6c0o-d 3bgr-d 5vqu-d 6c0n-d 4id5-d 6c0p-d 4idk-d 5vqr-d 6cgf-d 2hny-d 5vqx-d 4ify-d 5vqw-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) #227 - Nov 2018 Telomerase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #163 - Jul 2013 HIV Capsid similarity (1)

Deposited unit

A: REVERSE TRANSCRIPTASE/RIBONUCLEASE H, EXORIBONUCLEA P66 RT

B: P51 RT

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

Unit cell

Length a, b, c (Å)	161.408, 73.145, 108.768
Angle α, β, γ (deg.)	90.00, 100.47, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein , 2 types, 2 molecules AB

#1: Protein	REVERSE TRANSCRIPTASE/RIBONUCLEASE H, EXORIBONUCLEA P66 RT / GAG-POL POLYPROTEIN Mass: 63989.238 Da / Num. of mol.: 1 / Fragment: p66 / Mutation: K172A, K173A, C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 / Strain: BH10 / Gene: GAG-POL, POL / Plasmid: PCDF-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(RIL) References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H
#2: Protein	P51 RT / Gag-Pol polyprotein Mass: 50096.539 Da / Num. of mol.: 1 / Fragment: p51 RT / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 / Strain: BH10 / Gene: GAG-POL, POL / Plasmid: PCDF-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(RIL) / References: UniProt: P03366

#1: Protein

REVERSE TRANSCRIPTASE/RIBONUCLEASE H, EXORIBONUCLEA P66 RT / GAG-POL POLYPROTEIN

Mass: 63989.238 Da / Num. of mol.: 1 / Fragment: p66 / Mutation: K172A, K173A, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 / Strain: BH10 / Gene: GAG-POL, POL / Plasmid: PCDF-2 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(RIL)
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H

#2: Protein

P51 RT / Gag-Pol polyprotein

Mass: 50096.539 Da / Num. of mol.: 1 / Fragment: p51 RT / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 / Strain: BH10 / Gene: GAG-POL, POL / Plasmid: PCDF-2 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(RIL) / References: UniProt: P03366

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Non-polymers , 4 types, 671 molecules

#3: Chemical	ChemComp-1QP / ethyl pyrazolo[1,5-a]pyridine-3-carboxylate Mass: 190.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₀N₂O₂
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: 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*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 659 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.77 Å³/Da / Density % sol: 55.55 %
Crystal grow	Method: vapor diffusion, hanging drop / pH: 6.7 Details: 11% PEG 8000, 4% PEG 400, 50 MM IMIDAZOLE, 10 MM SPERMINE, 15 MM MGSO4, 100 MM AMMONIUM SULFATE, AND 5 MM TRIS(2-CARBOXYETHYL)PHOSPHINE, pH 6.7, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

CHESS

/ Beamline: F1 / Wavelength: 0.918 / Wavelength: 0.917 Å

Detector

Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 2, 2010

Radiation

Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.918	1
2	0.917	1

Reflection

Resolution: 1.854→43.297 Å / Num. obs: 105443 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / R_merge(I) obs: 0.065 / Net I/σ(I): 13.79

Reflection shell

Resolution: 1.85→1.88 Å / % possible all: 86.3

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.8.1_1168)	model building
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	1.8.1_1168	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.854→43.297 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 23.02 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2144	2052	2 %
R_work	0.1856	-	-
obs	0.1862	102628	97.03 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.854→43.297 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7929	0	82	659	8670

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8238
X-RAY DIFFRACTION	f_angle_d	1.201	11187
X-RAY DIFFRACTION	f_dihedral_angle_d	14.162	3113
X-RAY DIFFRACTION	f_chiral_restr	0.091	1203
X-RAY DIFFRACTION	f_plane_restr	0.007	1404

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 (%)
1.8539-1.897	0.341	107	0.2856	6050	X-RAY DIFFRACTION	88
1.897-1.9444	0.3136	117	0.2499	6453	X-RAY DIFFRACTION	94
1.9444-1.997	0.2808	134	0.2259	6430	X-RAY DIFFRACTION	94
1.997-2.0557	0.2547	130	0.2172	6559	X-RAY DIFFRACTION	95
2.0557-2.1221	0.2546	150	0.2004	6601	X-RAY DIFFRACTION	96
2.1221-2.1979	0.1996	132	0.1877	6704	X-RAY DIFFRACTION	97
2.1979-2.2859	0.2043	141	0.1896	6700	X-RAY DIFFRACTION	97
2.2859-2.39	0.2187	134	0.1905	6811	X-RAY DIFFRACTION	99
2.39-2.516	0.2538	142	0.1959	6836	X-RAY DIFFRACTION	99
2.516-2.6736	0.2241	143	0.1904	6776	X-RAY DIFFRACTION	98
2.6736-2.88	0.2183	147	0.1875	6811	X-RAY DIFFRACTION	99
2.88-3.1697	0.2096	156	0.1927	6908	X-RAY DIFFRACTION	100
3.1697-3.6282	0.2123	138	0.178	6907	X-RAY DIFFRACTION	100
3.6282-4.5703	0.1787	139	0.1584	6977	X-RAY DIFFRACTION	100
4.5703-43.3083	0.2037	142	0.1796	7053	X-RAY DIFFRACTION	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	0.6803	-0.0687	-0.4255	0.4083	0.8763	2.6772	0.0832	-0.2546	-0.1381	0.2425	0.0625	0.0927	0.2897	0.0504	-0.0773	0.4359	0.0124	0.0281	0.2746	0.058	0.2652	47.6028	-18.1924	60.0753
2	2.0692	1.0572	0.9365	1.8637	0.3181	2.3113	0.3784	-0.5591	-0.6975	0.4072	0.0943	0.3667	0.3117	-0.5972	-0.132	0.406	-0.0352	0.0439	0.288	0.1094	0.2929	36.6501	-26.8525	38.2366
3	1.5184	-1.1454	1.0269	1.064	-0.6917	0.6513	0.0364	-0.1115	-0.2185	0.0476	0.1105	0.2185	0.0996	-0.1612	-0.0701	0.1687	-0.006	0.0222	0.2062	-0.0126	0.2205	28.3442	-8.4115	14.0143
4	4.0571	0.6655	0.2276	2.7078	0.1542	3.4421	-0.0386	-0.2711	0.044	0.09	0.0595	0.1404	-0.1359	-0.2311	-0.0386	0.1026	0.0313	0.0322	0.2326	0.0045	0.2163	14.0933	9.266	6.8329
5	3.7198	-0.6436	0.5767	3.3998	0.2822	3.3898	-0.0738	0.0814	0.2475	0.2717	-0.0844	-0.137	-0.3353	0.3231	-0.0735	0.2324	-0.0764	-0.0221	0.164	0.0315	0.1707	56.3348	1.6736	36.407
6	5.0766	2.5604	-3.4481	7.818	-3.87	3.0014	0.0285	-0.8006	0.6233	1.6791	-0.577	-0.319	-1.8087	1.2689	-0.1062	0.9624	-0.3184	-0.3795	0.5068	0.1122	0.8468	55.9518	26.6125	33.6258
7	1.5765	-0.9577	1.1239	2.0318	-0.5879	1.4066	-0.2681	0.3572	0.6425	0.4215	-0.1604	-0.6785	-0.5229	0.6432	0.0144	0.5058	-0.2689	-0.1369	0.3876	0.125	0.4787	62.3737	12.6158	34.1772
8	2.0402	0.1005	1.271	1.1418	-0.2061	0.562	-0.1676	0.1149	-0.1308	0.3664	-0.2243	-0.7291	-0.3047	0.7355	0.1499	0.3489	-0.1432	-0.0147	1.0836	0.2515	0.6971	59.4263	20.414	14.4893
9	1.8027	0.2908	2.0232	2.5895	-0.064	3.8872	-0.2044	-0.0081	0.3704	0.2506	-0.0673	-0.0388	-0.3494	0.0228	0.2637	0.1927	-0.0556	0.0608	0.1965	-0.0212	0.1943	32.1082	25.3055	8.5783
10	3.4215	0.066	0.7818	5.2659	-0.5507	1.7754	0.101	0.0849	0.2299	0.1354	-0.259	-0.0443	-0.1686	0.0989	0.13	0.1976	-0.0384	0.0177	0.1774	-0.0055	0.1165	43.1787	10.6658	20.1937

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 194 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 195 through 296 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 297 through 473 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 474 through 554 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 5 through 83 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 84 through 104 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 105 through 194 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 195 through 253 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 254 through 363 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 364 through 428 )

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