4RFN

Crystal structure of ADCC-potent Rhesus macaque ANTIBODY JR4 in complex with HIV-1 CLADE A/E GP120 and M48


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.332 
  • R-Value Work: 0.273 

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 93TH057 (H375S) GP120
G, A
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
FAB HEAVY CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4
H, B
233N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FAB LIGHT CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4
L, C
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
T-CELL SURFACE GLYCOPROTEIN CD4 mimetic M48
M, D
28N/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, G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
D, M
NON-POLYMERH2 N

--

DPR
Query on DPR
D, M
D-PEPTIDE LINKINGC5 H9 N O2

--

MPT
Query on MPT
D, M
NON-POLYMERC3 H6 O2 S

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.332 
  • R-Value Work: 0.273 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 110.255α = 90.00
b = 77.827β = 114.26
c = 127.587γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data scaling
PHASERphasing
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