1RZ7

CRYSTAL STRUCTURE OF HUMAN ANTI-HIV-1 GP120-REACTIVE ANTIBODY 48D

> Summary

Summary for 1RZ7

Related1RZ8 1RZF 1RZG 1RZI 1RZJ 1RZK
DescriptorFab 48d 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 chains2
Total molecular weight46663.23
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 outliers0.23290.5%0.8%7.9%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1rz7
no rotation
Molmil generated image of 1rz7
rotated about x axis by 90°
Molmil generated image of 1rz7
rotated about y axis by 90°

> Structural details

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight46479.0
Non-Polymers*Number of molecules2
Total molecular weight184.2
All*Total molecular weight46663.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2 Å)

Cell axes63.48572.951101.921
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits20.00 - 2.00
the highest resolution shell value2.130 - 2.000
R-factor0.2011
R-work0.20100
the highest resolution shell value0.222
R-free0.23100
the highest resolution shell value0.255
RMSD bond length0.005
RMSD bond angle1.400 (1.386*)

Data Collection Statistics

Resolution limits20.00 - 2.00
the highest resolution shell value -
Number of reflections32647
Number of measurements230911*
Rmerge_l_obs0.060*
Completeness100.0 (99.8*)
the highest resolution shell value100.*
I/sigma(I)-3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP5.6 (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)
51reservoirPEG40008.3 (%)
61reservoirisopropyl alcohol8.3 (%)
71reservoir0.33 (M)
81reservoirsodium citrate0.04 (M)pH5.6
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
AC112BINDING SITE FOR RESIDUE GOL H 214
ChainResidue
HPHE172
HPRO173
HVAL175
HSER183
HLEU184
HSER185
HHOH
LGLN159
LSER161
LSER175
LSER176
LTHR177

AC27BINDING SITE FOR RESIDUE GOL L 214
ChainResidue
LGLN37
LLYS45
LLEU47
LARG61
LPHE62
LGLU81
LASP82

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

site_idNumber of ResiduesDetails
GOL_1rz7_L_21410GLYCEROL binding site
ChainResidueligand
LGLN37GOL: GLYCEROL
LLYS39GOL: GLYCEROL
LLYS45GOL: GLYCEROL
LLEU47GOL: GLYCEROL
LVAL58-PRO59GOL: GLYCEROL
LARG61-PHE62GOL: GLYCEROL
LGLU81-ASP82GOL: GLYCEROL

GOL_1rz7_H_21414GLYCEROL binding site
ChainResidueligand
LGLN160-SER162GOL: GLYCEROL
LSER176-THR178GOL: GLYCEROL
HLEU141GOL: GLYCEROL
HPHE166-VAL169GOL: GLYCEROL
HSER177-SER179GOL: GLYCEROL

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
PS002901Immunoglobulins and major histocompatibility complex proteins signature. [FY]-{L}-C-{PGAD}-[VA]-{LC}-H
ChainResidueDetails
HNA*

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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

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