1N0X

Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a Peptide Mimotope


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.252 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CXSClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a Peptide Mimotope

Saphire, E.O.Montero, M.Menendez, A.Irving, M.B.Zwick, M.B.Parren, P.W.H.I.Burton, D.R.Scott, J.K.Wilson, I.A.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IMMUNOGLOBULIN LIGHT CHAINA [auth L],
C [auth M]
215Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens)
Explore P01834 
Go to UniProtKB:  P01834
PHAROS:  P01834
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01834
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IMMUNOGLOBULIN HEAVY CHAINB [auth H],
D [auth K]
230Homo sapiensMutation(s): 0 
UniProt
Find proteins for P0DOX5 (Homo sapiens)
Explore P0DOX5 
Go to UniProtKB:  P0DOX5
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UniProt GroupP0DOX5
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
B2.1 peptideE [auth P],
F [auth R]
21synthetic constructMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CXS
Query on CXS

Download Ideal Coordinates CCD File 
I [auth H]3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
C9 H19 N O3 S
PJWWRFATQTVXHA-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H,
N [auth K],
S [auth R],
T [auth R]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth L]
J [auth H]
K [auth H]
L [auth M]
M
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
R [auth P]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ORN
Query on ORN
E [auth P],
F [auth R]
L-PEPTIDE LINKINGC5 H12 N2 O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.252 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.621α = 90
b = 184.358β = 103.05
c = 56.173γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CXSClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-13
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-06-21
    Changes: Advisory, Database references, Experimental preparation, Source and taxonomy, Structure summary