4RFO

Crystal structure of the ADCC-Potent Antibody N60-I3 Fab in complex with HIV-1 Clade A/E gp120 and M48u1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Cocrystal Structures of Antibody N60-i3 and Antibody JR4 in Complex with gp120 Define More Cluster A Epitopes Involved in Effective Antibody-Dependent Effector Function against HIV-1.

Gohain, N.Tolbert, W.D.Acharya, P.Yu, L.Liu, T.Zhao, P.Orlandi, C.Visciano, M.L.Kamin-Lewis, R.Sajadi, M.M.Martin, L.Robinson, J.E.Kwong, P.D.DeVico, A.L.Ray, K.Lewis, G.K.Pazgier, M.

(2015) J.Virol. 89: 8840-8854


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 clade A/E gp120
G
353Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q0ED31 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q0ED31
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
m48u1 CD4 mimetic peptide
N
28N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
N60-i3 Fab heavy chain
H
229N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
N60-i3 Fab light chain
L
221N/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 
G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001094
Query on PRD_001094
NCD4-MIMETIC MINIPROTEIN M48U1Peptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 98.305α = 90.00
b = 102.575β = 90.00
c = 108.038γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-08-19
    Type: Database references