1RZG

Crystal structure of Human anti-HIV-1 GP120 reactive antibody 412d

> Summary

Summary for 1RZG

Related1RZ7 1RZ8 1RZF 1RZI 1RZJ 1RZK
DescriptorFab 412d light and heavy chains
Functional Keywordshiv-1; gp120; cd4i; antibodies; tyrosine sulfation; vh-gene usage, immune system
Biological sourceHomo sapiens (human)
Total number of polymer chains4
Total molecular weight99003.28
Authors
Primary citation
Huang, C.C.,Venturi, M.,Majeed, S.,Moore, M.J.,Phogat, S.,Zhang, M.-Y.,Dimitrov, D.S.,Hendrickson, W.A.,Robinson, J.,Sodroski, J.,Wyatt, R.,Choe, H.,Farzan, M.,Kwong, P.D.
Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120
Proc.Natl.Acad.Sci.USA, 101:2706-2711, 2004
PubMed: 14981267
DOI: 10.1073/pnas.0308527100
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.251120.5%1.9%7.8%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1rzg
no rotation
Molmil generated image of 1rzg
rotated about x axis by 90°
Molmil generated image of 1rzg
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 1rzg
no rotation
Molmil generated image of 1rzg
rotated about x axis by 90°
Molmil generated image of 1rzg
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 (1rzg.pdb1.gz [79.36 KB])
Coordinate files for Biological unit (1rzg.pdb2.gz [76.43 KB])

> Structural details

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight96486.0
Non-Polymers*Number of molecules8
Total molecular weight2517.2
All*Total molecular weight99003.3
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2 Å)

Cell axes63.08889.31385.863
Cell angles90.00110.3190.00
SpacegroupP 1 21 1
Resolution limits20.00 - 2.00
the highest resolution shell value2.130 - 2.000
R-factor0.2011
R-work0.20100
the highest resolution shell value0.282
R-free0.25100
the highest resolution shell value0.328
RMSD bond length0.006
RMSD bond angle1.400 (1.395*)

Data Collection Statistics

Resolution limits20.00 (30.00*) - 1.90
the highest resolution shell value -
Number of reflections69755 (66722*)
Number of measurements209967*
Rmerge_l_obs0.069*
Completeness92.5*
the highest resolution shell value58.4*
I/sigma(I)-3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP6 (7.0*)293unknown*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11dropTris-HCl2.5 (mM)
21drop0.35 (M)
31drop0.02 (%(v/v))pH7.0
41dropprotein4-8 (mg/ml)
51reservoirPEG400018 (%)
61reservoir0.1 (M)
71reservoir0.02 (M)
81reservoirsodium acetate0.3 (M)pH6.0
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC111BINDING SITE FOR RESIDUE SUC A 9001
ChainResidue
ATYR60
AGLN65
AGLY66
AARG67
AVAL68
ASER69
ASUC
AHOH
AHOH
AHOH
AHOH

AC215BINDING SITE FOR RESIDUE SUC A 9002
ChainResidue
AARG38
AGLN43
AGLY44
ALEU45
AGLU46
AARG63
AHOH
AHOH
AHOH
AHOH
AHOH
BTHR97
BPHE98
BGLN100
BHOH

AC312BINDING SITE FOR RESIDUE SUC D 9003
ChainResidue
CARG38
CGLN43
CGLY44
CLEU45
CGLU46
CHOH
DTHR97
DPHE98
DGLN100
DHOH
DHOH
DHOH

AC49BINDING SITE FOR RESIDUE SUC C 9004
ChainResidue
CTYR60
CGLN65
CGLY66
CARG67
CVAL68
CSER69
CSUC
CHOH
CHOH

AC510BINDING SITE FOR RESIDUE SUC A 9005
ChainResidue
AASN56
ASER69
AILE70
ATHR71
ASUC
AHOH
AHOH
AHOH
AHOH
AHOH

AC66BINDING SITE FOR RESIDUE SUC C 9006
ChainResidue
CASN56
CTYR60
CSER69
CILE70
CSUC
CHOH

AC710BINDING SITE FOR RESIDUE SUC A 9007
ChainResidue
AGLY112
AMET113
ASER114
ATRP115
AHOH
BTRP32
BLYS50
BHIS91
BASP92
BHOH

AC83BINDING SITE FOR RESIDUE CYS D 9004
ChainResidue
DCYS214
DASP
DHOH

AC94BINDING SITE FOR RESIDUE ASP D 9005
ChainResidue
DCYS
DHOH
DHOH
DHOH

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

site_idNumber of ResiduesDetails
SUC_1rzg_A_900213SUCROSE binding site
ChainResidueligand
AARG38SUC: SUCROSE
AGLN43-TRP47SUC: SUCROSE
AARG62-PHE63SUC: SUCROSE
BTYR96-GLN100SUC: SUCROSE

SUC_1rzg_A_90057SUCROSE binding site
ChainResidueligand
AILE51SUC: SUCROSE
AASN55SUC: SUCROSE
AALA57SUC: SUCROSE
ATYR59SUC: SUCROSE
ASER68-THR70SUC: SUCROSE

SUC_1rzg_A_90019SUCROSE binding site
ChainResidueligand
AALA57SUC: SUCROSE
ATYR59SUC: SUCROSE
APHE63-ILE69SUC: SUCROSE

SUC_1rzg_A_900710SUCROSE binding site
ChainResidueligand
ATYS100SUC: SUCROSE
AGLY100SUC: SUCROSE
BTRP32SUC: SUCROSE
BLYS50SUC: SUCROSE
BHIS91-ASP92SUC: SUCROSE
BTYR96SUC: SUCROSE

SUC_1rzg_D_900312SUCROSE binding site
ChainResidueligand
CARG38SUC: SUCROSE
CGLN43-TRP47SUC: SUCROSE
CARG62SUC: SUCROSE
DTYR96-GLN100SUC: SUCROSE

SUC_1rzg_C_90067SUCROSE binding site
ChainResidueligand
CILE51SUC: SUCROSE
CASN55SUC: SUCROSE
CALA57SUC: SUCROSE
CTYR59SUC: SUCROSE
CSER68-THR70SUC: SUCROSE

SUC_1rzg_C_90049SUCROSE binding site
ChainResidueligand
CALA57SUC: SUCROSE
CTYR59SUC: SUCROSE
CPHE63-ILE69SUC: SUCROSE

CYS_1rzg_D_90041CYSTEINE binding site
ChainResidueligand
DCYS214CYS: CYSTEINE

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
PS002902Immunoglobulins and major histocompatibility complex proteins signature. [FY]-{L}-C-{PGAD}-[VA]-{LC}-H
ChainResidueDetails
BNA*
DNA*

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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
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb1rzg.ent.gz (157.12 KB)
Display
all (no-compress)pdb1rzg.ent (655.04 KB)
header onlypdb1rzg.ent.gz (8.91 KB)
Display
PDBx/mmCIF1rzg.cif.gz (196.1 KB)
PDBMLall1rzg.xml.gz (300.73 KB)
Display
no-atom1rzg-noatom.xml.gz (45.41 KB)
Display
ext-atom1rzg-extatom.xml.gz (173.73 KB)
Display
PDBMLplusall1rzg-plus.xml.gz (303.6 KB)
Display
no-atom1rzg-plus-noatom.xml.gz (48.28 KB)
Display
add only1rzg-add.xml.gz (2.87 KB)
Display
RDF1rzg.rdf.gz (85.92 KB)
Display
Structure factorsr1rzgsf.ent.gz (993.99 KB)
Biological unit (PDB format)1rzg.pdb1.gz (79.36 KB) (A,B)
*author and software defined assembly, 2 molecule(s) (dimeric)
Display
1rzg.pdb2.gz (76.43 KB) (C,D)
*author and software defined assembly, 2 molecule(s) (dimeric)
Display
Validation reportsPDF1rzg​_validation.pdf.gz (331.16 KB)
Display
PDF-full1rzg​_full​_validation.pdf.gz (350.63 KB)
Display
XML1rzg​_validation.xml.gz (45.05 KB)
Display
PNG1rzg​_multipercentile​_validation.png.gz (152.42 KB)
Display
SVG1rzg​_multipercentile​_validation.svg.gz (951 B)
Display
Sequence (fasta)1rzg​_seq.txt
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