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- PDB-5u6e: Crystal structure of clade A/E HIV-1 gp120 core in complex with N... -

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Basic information

Entry
Database: PDB / ID: 5u6e
TitleCrystal structure of clade A/E HIV-1 gp120 core in complex with NBD-14010
Componentsclade A/E 93TH057 HIV-1 gp120 core
KeywordsVIRAL PROTEIN / HIV-1 / NBD-14010 / virus entry antagonist / small molecule
Function / homology
Function and homology information


HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Chem-82M / clade A/E 93TH057 HIV-1 gp120 core
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.095 Å
AuthorsKwon, Y.D. / Debnath, A.K. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)W-31-109-Eng-38 United States
CitationJournal: J. Med. Chem. / Year: 2017
Title: Synthesis, Antiviral Potency, in Vitro ADMET, and X-ray Structure of Potent CD4 Mimics as Entry Inhibitors That Target the Phe43 Cavity of HIV-1 gp120.
Authors: Curreli, F. / Kwon, Y.D. / Belov, D.S. / Ramesh, R.R. / Kurkin, A.V. / Altieri, A. / Kwong, P.D. / Debnath, A.K.
History
DepositionDec 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: clade A/E 93TH057 HIV-1 gp120 core
B: clade A/E 93TH057 HIV-1 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,59724
Polymers78,3212
Non-polymers5,27622
Water3,495194
1
A: clade A/E 93TH057 HIV-1 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,24114
Polymers39,1601
Non-polymers3,08013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: clade A/E 93TH057 HIV-1 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,35610
Polymers39,1601
Non-polymers2,1969
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.181, 68.743, 94.749
Angle α, β, γ (deg.)90.00, 91.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein clade A/E 93TH057 HIV-1 gp120 core


Mass: 39160.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: clade A/E 93TH057 HIV-1 gp120 core, V1/V2 and V3 region deletion, H375S
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Plasmid: pVRC8400 / Cell line (production host): HEK 293 GNTI- / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-82M / N-{(1S)-2-amino-1-[5-(hydroxymethyl)-4-methyl-1,3-thiazol-2-yl]ethyl}-5-(4-chloro-3-fluorophenyl)-1H-pyrrole-2-carboxamide


Mass: 408.878 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18ClFN4O2S
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 10-16% PEG 3350, 5% Iso-propanol, 0.1M HEPES, 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 49455 / % possible obs: 96.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 43.6 Å2 / Rsym value: 0.089 / Net I/σ(I): 13.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 1.56 / % possible all: 81

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DKQ

4dkq


Resolution: 2.095→37.917 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.81
RfactorNum. reflection% reflection
Rfree0.2311 2330 4.9 %
Rwork0.1926 --
obs0.1944 47507 96.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.095→37.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5320 0 336 194 5850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055804
X-RAY DIFFRACTIONf_angle_d0.77922
X-RAY DIFFRACTIONf_dihedral_angle_d11.7973460
X-RAY DIFFRACTIONf_chiral_restr0.053926
X-RAY DIFFRACTIONf_plane_restr0.0041000
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.095-2.13780.28461000.28362099X-RAY DIFFRACTION76
2.1378-2.18430.3351180.26742390X-RAY DIFFRACTION88
2.1843-2.23510.27261590.25542553X-RAY DIFFRACTION93
2.2351-2.2910.2861370.23472676X-RAY DIFFRACTION97
2.291-2.35290.27991180.23852717X-RAY DIFFRACTION99
2.3529-2.42210.26051180.23352790X-RAY DIFFRACTION99
2.4221-2.50030.28611540.2342695X-RAY DIFFRACTION99
2.5003-2.58960.25281530.21692684X-RAY DIFFRACTION99
2.5896-2.69330.25851350.21552738X-RAY DIFFRACTION99
2.6933-2.81580.25591540.21842695X-RAY DIFFRACTION99
2.8158-2.96420.25851630.21522748X-RAY DIFFRACTION99
2.9642-3.14980.25811740.20072682X-RAY DIFFRACTION99
3.1498-3.39290.21711440.19482722X-RAY DIFFRACTION99
3.3929-3.73410.251200.18112730X-RAY DIFFRACTION98
3.7341-4.27380.22051070.16172778X-RAY DIFFRACTION98
4.2738-5.3820.17291540.15662717X-RAY DIFFRACTION98
5.382-37.9230.21831220.18982763X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.54360.41812.0224.03260.12985.2699-0.10810.020.34020.2865-0.0463-0.138-0.37810.1320.13390.2435-0.01690.03820.2786-0.03070.416218.24045.075440.5874
20.7732-0.55380.58585.0374-1.78762.6059-0.1590.06480.18290.3343-0.2428-0.8977-0.02570.43410.12440.22130.03320.04210.3560.03090.503223.767-2.619742.934
32.7273-2.34551.27797.9835-1.4054.8301-0.1899-0.04490.55840.32910.06430.1224-0.5772-0.35860.04920.06280.01450.05550.3195-0.00840.377411.1823-0.058937.1745
41.40780.02851.14634.81880.07233.0016-0.027-0.2090.1323-0.16550.14270.38240.1721-0.1641-0.13850.2320.04770.02080.3442-0.06440.34078.9857-12.185633.8006
54.1248-1.444.85482.815-0.87039.126-0.1411-0.652-0.3050.36060.16590.23740.3659-0.59-0.14170.3732-0.02290.11640.4073-0.00660.390810.4392-22.574446.5645
66.14790.33675.80472.31260.65996.96290.32990.2078-0.1838-0.0446-0.0078-0.32740.52390.355-0.31080.33820.05260.08640.29630.00960.391718.2627-21.929339.2392
74.49471.60982.70658.03540.06688.3242-0.1533-0.1874-0.6857-0.35510.14090.30050.286-0.6667-0.07390.35720.0070.0690.37950.01270.423712.8779-28.285645.2501
82.9628-0.26831.31132.4448-0.94052.7774-0.00560.05910.0341-0.0021-0.0681-0.4540.2350.33920.070.25230.07440.08750.3255-0.03280.452721.3236-19.024439.9977
98.0007-3.56972.77433.1766-4.47347.73380.2230.37730.0983-0.2419-0.31840.3042-0.09380.01910.10520.21840.00620.06180.2859-0.06780.332215.25721.284733.5283
103.9892-1.1122-1.11363.6855-0.76822.64680.13560.11420.251-0.51510.21330.3923-0.0906-0.6646-0.36130.69210.0178-0.13670.46710.11990.4064-11.9963-13.68919.844
113.8786-0.9597-2.78270.9452.84658.73710.21950.8899-0.0725-1.272-0.2683-0.10180.75460.01030.01281.29780.15270.07280.53630.0210.44834.1171-26.6125-2.2084
126.77680.79020.91998.5184-1.76152.35360.3797-0.42070.534-0.13490.381.69930.2661-1.0217-0.83150.54290.0257-0.08990.62450.11320.5968-20.7208-13.997615.1118
137.1879-3.6844-0.83429.26960.80554.1861-0.1375-0.55990.0997-0.0810.61220.59420.2739-0.9791-0.38650.4981-0.0196-0.08410.56520.20820.263-17.2757-19.363514.996
146.462-1.05630.08081.54771.8845.2154-0.0604-0.3452-0.6739-0.56240.48191.08830.8097-1.3883-0.29360.8215-0.343-0.29840.77410.31480.7092-20.4513-31.668415.3962
159.09860.36730.39845.0323-0.52973.53860.1976-1.297-1.065-0.37480.32580.58991.3616-0.3167-0.27241.2071-0.2018-0.23110.4510.24320.5664-7.4018-41.32618.7333
162.429-0.6116-0.38373.4384-0.53572.45990.03470.2467-1.0098-0.88660.41870.37261.4676-0.8392-0.31871.4757-0.3567-0.33170.59170.1170.6775-10.611-41.50889.1174
173.9301-2.05681.32122.42710.96782.60840.48610.1543-0.7846-1.09970.11210.63661.2211-0.3069-0.26781.506-0.112-0.31880.36260.02090.6279-4.6703-40.93737.5898
181.6818-1.5380.04472.5735-0.4124.43610.0391-0.159-0.4067-0.73160.28580.08551.0678-0.0056-0.36390.9248-0.0372-0.15530.2918-0.04390.3987-2.0701-35.210511.5172
195.08121.383-4.96348.5579-4.65846.2014-0.66750.7216-2.1955-0.72010.64820.3293-0.3199-1.12550.0971.483-0.4983-0.40731.02510.11021.3274-25.1411-44.6687.6394
206.0937-3.5271-1.11242.49282.14746.16090.13940.29730.2464-0.32480.35640.48180.3107-0.9059-0.41230.5118-0.1294-0.16020.62780.25910.5993-19.2477-17.97949.8783
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 115 )
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 235 )
3X-RAY DIFFRACTION3chain 'A' and (resid 236 through 258 )
4X-RAY DIFFRACTION4chain 'A' and (resid 259 through 291 )
5X-RAY DIFFRACTION5chain 'A' and (resid 292 through 352 )
6X-RAY DIFFRACTION6chain 'A' and (resid 353 through 385 )
7X-RAY DIFFRACTION7chain 'A' and (resid 386 through 421 )
8X-RAY DIFFRACTION8chain 'A' and (resid 422 through 474 )
9X-RAY DIFFRACTION9chain 'A' and (resid 475 through 492 )
10X-RAY DIFFRACTION10chain 'B' and (resid 44 through 115 )
11X-RAY DIFFRACTION11chain 'B' and (resid 116 through 215 )
12X-RAY DIFFRACTION12chain 'B' and (resid 216 through 235 )
13X-RAY DIFFRACTION13chain 'B' and (resid 236 through 258 )
14X-RAY DIFFRACTION14chain 'B' and (resid 259 through 291 )
15X-RAY DIFFRACTION15chain 'B' and (resid 292 through 352 )
16X-RAY DIFFRACTION16chain 'B' and (resid 353 through 390 )
17X-RAY DIFFRACTION17chain 'B' and (resid 391 through 434 )
18X-RAY DIFFRACTION18chain 'B' and (resid 435 through 456 )
19X-RAY DIFFRACTION19chain 'B' and (resid 457 through 474 )
20X-RAY DIFFRACTION20chain 'B' and (resid 475 through 492 )

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