2QAD

Structure of tyrosine-sulfated 412d antibody complexed with HIV-1 YU2 gp120 and CD4

Structural Biology Knowledgebase: 2QAD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.202

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2QAD

Classification: viral protein / immune system

Total Structure Weight: 216739.22

Macromolecule Entities
Molecule Chains Length Organism Details
Envelope glycoprotein gp160 A, E 322 Human immunodeficiency virus 1 Fragment: CORE WITH V3
Gene Name(s): env
T-cell surface glycoprotein CD4 B, F 181 Homo sapiens Fragment: D1D2, IG-LIKE V-TYPE AND IG-LIKE C2-TYPE 1 DOMAINS
Gene Name(s): CD4 Gene View
anti-HIV-1 antibody 412d light chain C, G 214 Homo sapiens Fragment: FAB, ANTIGEN-BINDING FRAGMENT
anti-HIV-1 antibody 412d heavy chain D, H 231 Homo sapiens Fragment: FAB, ANTIGEN-BINDING FRAGMENT
Gene Name(s): VHCH1

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

A, E N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MLA
Query on MLA

A, B, F, H MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID (Synonym)
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, C, D, E, F 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TYS
Query on TYS
D, H L-PEPTIDE LINKING C9 H11 N O6 S TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.202
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 109.60 α = 90.00
b = 53.02 β = 104.64
c = 225.33 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-06-14
  • Released Date: 2007-09-25
  • Deposition author(s): Huang, C.-C., Tang, M., Robinson, J., Wyatt, R., Kwong, P.D.

Revision History

  • 2015-04-29
    Type: Non-polymer description | Details: --
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4