4H8W

Crystal structure of non-neutralizing and ADCC-potent antibody N5-i5 in complex with HIV-1 clade A/E gp120 and sCD4.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Definition of an Antibody-Dependent Cellular Cytotoxicity Response Implicated in Reduced Risk for HIV-1 Infection.

Acharya, P.Tolbert, W.D.Gohain, N.Wu, X.Yu, L.Liu, T.Huang, W.Huang, C.C.Kwon, Y.D.Louder, R.K.Luongo, T.S.McLellan, J.S.Pancera, M.Yang, Y.Zhang, B.Flinko, R.Foulke, J.S.Sajadi, M.M.Kamin-Lewis, R.Robinson, J.E.Martin, L.Kwong, P.D.Guan, Y.DeVico, A.L.Lewis, G.K.Pazgier, M.

(2014) J.Virol. 88: 12895-12906


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 CLADE A/E 93TH057 (H375S) GP120
G
353Human immunodeficiency virus 1Gene Names: env
Find proteins for Q0ED31 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q0ED31
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FAB HEAVY CHAIN OF ADCC AND NON-NEUTRALIZING ANTI-HIV-1 ANTIBODY N5-I5
H
226N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FAB LIGHT CHAIN OF ADCC AND NON-NEUTRALIZING ANTI-HIV-1 ANTIBODY N5-I5
L
217N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD4
C
185Homo sapiensGene Names: CD4
Find proteins for P01730 (Homo sapiens)
Go to Gene View: CD4
Go to UniProtKB:  P01730
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MRD
Query on MRD

Download SDF File 
Download CCD File 
G, L
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 92.251α = 90.00
b = 103.909β = 90.00
c = 134.654γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
REFMACrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-10-15
    Type: Database references
  • Version 1.2: 2014-10-22
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description