2NY7

HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing CD4-Binding-Site Antibody b12

Structural Biology Knowledgebase: 2NY7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.193

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2NY7

Classification: VIRAL PROTEIN / IMMUNE SYSTEM

Total Structure Weight: 86621.33

Macromolecule Entities
Molecule Chains Length Organism Details
ENVELOPE GLYCOPROTEIN GP120 G 317 Human immunodeficiency virus 1 Fragment: CORE
Gene Name(s): env
ANTIBODY b12, HEAVY CHAIN H 230 Homo sapiens Fragment: ANTIGEN-BINDING FRAGMENT, FAB
ANTIBODY b12, LIGHT CHAIN L 215 Homo sapiens Fragment: ANTIGEN-BINDING FRAGMENT, FAB
Gene Name(s): IGKC

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

G N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.193
  • Space Group: P 65 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 101.96 α = 90.00
b = 101.96 β = 90.00
c = 298.29 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-11-20
  • Released Date: 2007-02-06
  • Deposition author(s): Zhou, T., Xu, L., Dey, B., Hessell, A.J., Van Ryk, D., Xiang, S.H., Yang, X., Zhang, M.Y., Zwick, M.B., Arthos, J., Burton, D.R., Dimitrov, D.S., Sodroski, J., Wyatt, R., Nabel, G.J., Kwong, P.D.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update