3TGS

Crystal structure of HIV-1 clade C strain C1086 gp120 core in complex with NBD-556

> Summary

Summary for 3TGS

Related3TGQ 3TGR 3TGT 3TIH
DescriptorHIV-1 clade C1086 gp120 core
Functional Keywordshiv-1 gp120, clade c1086, complex, nbd-556, viral protein
Biological sourceHuman immunodeficiency virus 1 (HIV-1)
Total number of polymer chains2
Total molecular weight83063.44
Authors
Kwon, Y.D.,Kwong, P.D. (deposition date: 2011-08-17, release date: 2012-04-04, modification date: 2014-12-17)
Primary citation
Kwon, Y.D.,Finzi, A.,Wu, X.,Dogo-Isonagie, C.,Lee, L.K.,Moore, L.R.,Schmidt, S.D.,Stuckey, J.,Yang, Y.,Zhou, T.,Zhu, J.,Vicic, D.A.,Debnath, A.K.,Shapiro, L.,Bewley, C.A.,Mascola, J.R.,Sodroski, J.G.,Kwong, P.D.
Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops.
Proc.Natl.Acad.Sci.USA, 109:5663-5668, 2012
PubMed: 22451932
DOI: 10.1073/pnas.1112391109
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.7 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.303190.6%4.4%10.3%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 3tgs
no rotation
Molmil generated image of 3tgs
rotated about x axis by 90°
Molmil generated image of 3tgs
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 3tgs
no rotation
Molmil generated image of 3tgs
rotated about x axis by 90°
Molmil generated image of 3tgs
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (3tgs.pdb1.gz [241.54 KB])
Coordinate files for Biological unit (3tgs.pdb2.gz [241.54 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BHIV-1 clade C1086 gp120 corepolymer35839756.02
Pfam (PF00516)
UniProt (by SIFTS) (C6G099)
Human immunodeficiency virus 1 (HIV-1)
SUGAR (N-ACETYL-D-GLUCOSAMINE)non-polymer221.213
N-(4-CHLOROPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDEnon-polymer337.82
waterwater18.0104

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight79512.0
Non-Polymers*Number of molecules15
Total molecular weight3551.4
All*Total molecular weight83063.4
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.7 Å)

Cell axes66.960126.000191.480
Cell angles90.0090.0090.00
SpacegroupC 2 2 21
Resolution limits44.84 - 2.70
the highest resolution shell value2.842 - 2.675
R-factor0.2422
R-work0.23940
the highest resolution shell value0.369
R-free0.29540
the highest resolution shell value0.461
RMSD bond length0.010
RMSD bond angle0.699

Data Collection Statistics

Resolution limits50.00 - 2.70
the highest resolution shell value -
Number of reflections17560
Rmerge_l_obs0.116
the highest resolution shell value0.222
Completeness74.0
Redundancy5.2
the highest resolution shell value3.6
I/sigma(I)0

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP6.5293

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0044175cellular_componenthost cell endosome membrane
A0020002cellular_componenthost cell plasma membrane
A0016021cellular_componentintegral component of membrane
A0019031cellular_componentviral envelope
A0055036cellular_componentvirion membrane
A0005198molecular_functionstructural molecule activity
A0006915biological_processapoptotic process
A0039663biological_processmembrane fusion involved in viral entry into host cell
A0019062biological_processvirion attachment to host cell
B0044175cellular_componenthost cell endosome membrane
B0020002cellular_componenthost cell plasma membrane
B0016021cellular_componentintegral component of membrane
B0019031cellular_componentviral envelope
B0055036cellular_componentvirion membrane
B0005198molecular_functionstructural molecule activity
B0006915biological_processapoptotic process
B0039663biological_processmembrane fusion involved in viral entry into host cell
B0019062biological_processvirion attachment to host cell
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC15BINDING SITE FOR RESIDUE NAG A 501
ChainResidue
AASN234
ATHR236
APRO238
AILE272
ALEU277

AC25BINDING SITE FOR RESIDUE NAG A 502
ChainResidue
AASN262
ACYS445
AASN446
ASER447
ANAG509

AC34BINDING SITE FOR RESIDUE NAG A 503
ChainResidue
AASN276
ATHR278
AASN279
BTHR278

AC45BINDING SITE FOR RESIDUE NAG A 504
ChainResidue
AGLU268
AILE270
AASN289
ALYS344
AGLU348

AC58BINDING SITE FOR RESIDUE NAG A 505
ChainResidue
AGLU335
AGLU335
ASER336
AASN339
ATYR403
AARG408
ASER409
AGLY412

AC63BINDING SITE FOR RESIDUE NAG A 506
ChainResidue
ATHR373
AASN386
ASER388

AC713BINDING SITE FOR RESIDUE 03G A 507
ChainResidue
AVAL255
AGLU370
APHE376
AASN377
APHE382
AILE424
AASN425
AMET426
ATRP427
AGLU429
AGLY473
AMET475
AHOH635

AC85BINDING SITE FOR RESIDUE NAG A 508
ChainResidue
APRO363
AASP389
AASN392
AASN404
ATHR406

AC96BINDING SITE FOR RESIDUE NAG A 509
ChainResidue
AASN262
ASER291
AASN448
ANAG502
AHOH646
BGLU290

BC14BINDING SITE FOR RESIDUE NAG B 501
ChainResidue
BASN234
BTHR236
BPRO238
BSER274

BC212BINDING SITE FOR RESIDUE 03G B 502
ChainResidue
BVAL255
BPHE376
BASN377
BPHE382
BILE424
BASN425
BMET426
BTRP427
BVAL430
BGLY473
BASP474
BMET475

BC37BINDING SITE FOR RESIDUE NAG B 503
ChainResidue
BASP211
BVAL254
BASN262
BASN377
BCYS445
BASN446
BSER447

BC46BINDING SITE FOR RESIDUE NAG B 504
ChainResidue
AASN446
BGLU268
BGLU269
BASN289
BGLU290
BGLU348

BC53BINDING SITE FOR RESIDUE NAG B 505
ChainResidue
BASN386
BSER388
BHOH632

BC64BINDING SITE FOR RESIDUE NAG B 506
ChainResidue
BASP389
BASN392
BTHR406
BGLY407

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
NAG_3tgs_B_50313N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
AASP57NAG: N-ACETYL-D-GLUCOSAMINE
BASP211-PRO212NAG: N-ACETYL-D-GLUCOSAMINE
BLYS252NAG: N-ACETYL-D-GLUCOSAMINE
BVAL254NAG: N-ACETYL-D-GLUCOSAMINE
BLEU261-ASN262NAG: N-ACETYL-D-GLUCOSAMINE
BPHE376-CYS378NAG: N-ACETYL-D-GLUCOSAMINE
BCYS445-SER447NAG: N-ACETYL-D-GLUCOSAMINE

03G_3tgs_A_50721N-(4-CHLOROPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE binding site
ChainResidueligand
ATRP11203G: N-(4-CHLOROPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE
AVAL255-THR25703G: N-(4-CHLOROPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE
AGLU370-ILE37103G: N-(4-CHLOROPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE
ASER375-ASN37703G: N-(4-CHLOROPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE
APHE38203G: N-(4-CHLOROPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE
ATYR38403G: N-(4-CHLOROPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE
AILE424-VAL43003G: N-(4-CHLOROPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE
AGLY473-MET47503G: N-(4-CHLOROPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE

NAG_3tgs_A_50210N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
AASP211-PRO212NAG: N-ACETYL-D-GLUCOSAMINE
ALYS252NAG: N-ACETYL-D-GLUCOSAMINE
AVAL254NAG: N-ACETYL-D-GLUCOSAMINE
ALEU261-ASN262NAG: N-ACETYL-D-GLUCOSAMINE
AASN377NAG: N-ACETYL-D-GLUCOSAMINE
ACYS445-SER447NAG: N-ACETYL-D-GLUCOSAMINE

NAG_3tgs_A_5018N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
AASN234NAG: N-ACETYL-D-GLUCOSAMINE
ATHR236-PRO238NAG: N-ACETYL-D-GLUCOSAMINE
AILE272-SER274NAG: N-ACETYL-D-GLUCOSAMINE
ALEU277NAG: N-ACETYL-D-GLUCOSAMINE

NAG_3tgs_A_50911N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
ALYS252NAG: N-ACETYL-D-GLUCOSAMINE
AASN262NAG: N-ACETYL-D-GLUCOSAMINE
ALEU265NAG: N-ACETYL-D-GLUCOSAMINE
ASER291NAG: N-ACETYL-D-GLUCOSAMINE
AASN293NAG: N-ACETYL-D-GLUCOSAMINE
AASN446NAG: N-ACETYL-D-GLUCOSAMINE
AASN448NAG: N-ACETYL-D-GLUCOSAMINE
BGLU290NAG: N-ACETYL-D-GLUCOSAMINE
BLYS337NAG: N-ACETYL-D-GLUCOSAMINE
BASN340NAG: N-ACETYL-D-GLUCOSAMINE
BLYS344NAG: N-ACETYL-D-GLUCOSAMINE

NAG_3tgs_A_5047N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
AGLU268-ILE270NAG: N-ACETYL-D-GLUCOSAMINE
AASN289-GLU290NAG: N-ACETYL-D-GLUCOSAMINE
ALYS344NAG: N-ACETYL-D-GLUCOSAMINE
AGLU348NAG: N-ACETYL-D-GLUCOSAMINE

NAG_3tgs_A_5033N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
AASN276NAG: N-ACETYL-D-GLUCOSAMINE
ATHR278-ASN279NAG: N-ACETYL-D-GLUCOSAMINE

NAG_3tgs_A_5058N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
AGLU335-SER336NAG: N-ACETYL-D-GLUCOSAMINE
AASN339NAG: N-ACETYL-D-GLUCOSAMINE
ATYR403-HIS405NAG: N-ACETYL-D-GLUCOSAMINE
AARG408NAG: N-ACETYL-D-GLUCOSAMINE
AGLY412NAG: N-ACETYL-D-GLUCOSAMINE

NAG_3tgs_A_5089N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
APHE361-PRO363NAG: N-ACETYL-D-GLUCOSAMINE
ASER388-ASP389NAG: N-ACETYL-D-GLUCOSAMINE
APHE391-ASN392NAG: N-ACETYL-D-GLUCOSAMINE
ATHR406-GLY407NAG: N-ACETYL-D-GLUCOSAMINE

NAG_3tgs_A_5065N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
ALEU369NAG: N-ACETYL-D-GLUCOSAMINE
ATHR372-THR373NAG: N-ACETYL-D-GLUCOSAMINE
AASN386NAG: N-ACETYL-D-GLUCOSAMINE
ASER388NAG: N-ACETYL-D-GLUCOSAMINE

NAG_3tgs_B_5049N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
AASN446NAG: N-ACETYL-D-GLUCOSAMINE
BGLU267-ILE270NAG: N-ACETYL-D-GLUCOSAMINE
BASN289-GLU290NAG: N-ACETYL-D-GLUCOSAMINE
BLYS344NAG: N-ACETYL-D-GLUCOSAMINE
BGLU348NAG: N-ACETYL-D-GLUCOSAMINE

03G_3tgs_B_50221N-(4-CHLOROPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE binding site
ChainResidueligand
BTRP11203G: N-(4-CHLOROPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE
BVAL255-THR25703G: N-(4-CHLOROPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE
BGLU370-ILE37103G: N-(4-CHLOROPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE
BSER375-ASN37703G: N-(4-CHLOROPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE
BPHE38203G: N-(4-CHLOROPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE
BTYR38403G: N-(4-CHLOROPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE
BILE424-VAL43003G: N-(4-CHLOROPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE
BGLY473-MET47503G: N-(4-CHLOROPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE

NAG_3tgs_B_50110N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
BASN234NAG: N-ACETYL-D-GLUCOSAMINE
BTHR236-PRO238NAG: N-ACETYL-D-GLUCOSAMINE
BILE272NAG: N-ACETYL-D-GLUCOSAMINE
BSER274-LEU277NAG: N-ACETYL-D-GLUCOSAMINE
BHIS352NAG: N-ACETYL-D-GLUCOSAMINE

NAG_3tgs_B_5067N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
BGLU362-PRO363NAG: N-ACETYL-D-GLUCOSAMINE
BSER388-ASP389NAG: N-ACETYL-D-GLUCOSAMINE
BASN392NAG: N-ACETYL-D-GLUCOSAMINE
BTHR406-GLY407NAG: N-ACETYL-D-GLUCOSAMINE

NAG_3tgs_B_5057N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
BPRO363-SER364NAG: N-ACETYL-D-GLUCOSAMINE
BLEU369NAG: N-ACETYL-D-GLUCOSAMINE
BTHR372-THR373NAG: N-ACETYL-D-GLUCOSAMINE
BASN386NAG: N-ACETYL-D-GLUCOSAMINE
BSER388NAG: N-ACETYL-D-GLUCOSAMINE

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb3tgs.ent.gz (249.89 KB)
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all (no-compress)pdb3tgs.ent (965.67 KB)
header onlypdb3tgs.ent.gz (9.83 KB)
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PDBx/mmCIF3tgs.cif.gz (299.92 KB)
PDBMLall3tgs.xml.gz (454.12 KB)
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no-atom3tgs-noatom.xml.gz (35.74 KB)
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ext-atom3tgs-extatom.xml.gz (138.54 KB)
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PDBMLplusall3tgs-plus.xml.gz (457.63 KB)
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no-atom3tgs-plus-noatom.xml.gz (39.26 KB)
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add only3tgs-add.xml.gz (3.51 KB)
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RDF3tgs.rdf.gz (67.59 KB)
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Structure factorsr3tgssf.ent.gz (151.17 KB)
Biological unit (PDB format)3tgs.pdb1.gz (241.54 KB) (A,B)
*author and software defined assembly, 2 molecule(s) (dimeric)
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3tgs.pdb2.gz (241.54 KB) (B,A)
*author and software defined assembly, 2 molecule(s) (dimeric)
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Validation reportsPDF3tgs​_validation.pdf.gz (313.33 KB)
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PDF-full3tgs​_full​_validation.pdf.gz (341.15 KB)
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XML3tgs​_validation.xml.gz (33.62 KB)
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PNG3tgs​_multipercentile​_validation.png.gz (152.89 KB)
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SVG3tgs​_multipercentile​_validation.svg.gz (948 B)
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Sequence (fasta)3tgs​_seq.txt
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