4LAJ

Crystal structure of HIV-1 YU2 envelope gp120 glycoprotein in complex with CD4-mimetic miniprotein, M48U1, and llama single-domain, broadly neutralizing, co-receptor binding site antibody, JM4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.185

Literature

Macromolecules
Sequence Display for 4LAJ

Classification: VIRAL PROTEIN / INHIBITOR

Total Structure Weight: 243358.81

Macromolecule Entities
Molecule Chains Length Organism Details
HIV-1 YU2 gp120 envelope glycoprotein A, B, F, J 376 Human immunodeficiency virus 1 Gene Name(s): env
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CD4-mimetic miniprotein M48U1 C, D, G, K 28 synthetic
Llama single domain antibody, JM4 H, I, L, M 129 Lama glama Gene Name(s): hi113
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A, B, F, J N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACA
Query on ACA

B 6-AMINOHEXANOIC ACID
AMINOCAPROIC ACID (Synonym)
C6 H13 N O2
SLXKOJJOQWFEFD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B, J 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_001094
Query on PRD_001094
C, D, G, K CD4-MIMETIC MINIPROTEIN M48U1 Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.185
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 96.77 α = 90.00
b = 86.22 β = 102.88
c = 144.85 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-06-20
  • Released Date: 2013-08-14
  • Deposition author(s): Acharya, P., Luongo, T.S., Kwong, P.D.

Revision History

  • Version 1_0: 2013-08-14

    Type: Initial release

  • Version 1_1: 2013-08-21

    Type: Structure summary

  • Version 1_2: 2013-09-04

    Type: Database references

  • Version 1_3: 2014-04-09

    Type: Source and taxonomy