6A0Z

Crystal structure of broadly neutralizing antibody 13D4 bound to H5N1 influenza hemagglutinin, HA head region


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.329 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for the Broad, Antibody-Mediated Neutralization of H5N1 Influenza Virus.

Lin, Q.Li, T.Chen, Y.Lau, S.Y.Wei, M.Zhang, Y.Zhang, Z.Yao, Q.Li, J.Li, Z.Wang, D.Zheng, Q.Yu, H.Gu, Y.Zhang, J.Chen, H.Li, S.Xia, N.

(2018) J. Virol. 92: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin,Envelope glycoprotein
A
551Influenza A virusHuman immunodeficiency virus 1
This entity is chimeric
Mutation(s): 0 
Gene Names: HA,
Find proteins for Q6DQ34 (Influenza A virus)
Go to UniProtKB:  Q6DQ34
Find proteins for M1E1E4 (Human immunodeficiency virus 1)
Go to UniProtKB:  M1E1E4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antibody 13D4, Fab Heavy Chain
H
224N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Antibody 13D4, Fab Light Chain
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
H
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.329 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 72.245α = 90.00
b = 72.665β = 93.37
c = 76.704γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-06-06 
  • Released Date: 2018-06-20 
  • Deposition Author(s): Li, S., Li, T.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31670934
National Natural Science Foundation of ChinaChina30901077

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-07-25
    Type: Data collection, Database references
  • Version 1.2: 2018-09-19
    Type: Data collection, Database references