1YYM

crystal structure of F23, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120 envelope glycoprotein and anti-HIV-1 antibody 17b

Structural Biology Knowledgebase: 1YYM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.209

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YYM

Classification: Viral protein / Immune system

Total Structure Weight: 174904.17

Macromolecule Entities
Molecule Chains Length Organism Details
Exterior membrane glycoprotein(GP120) G, P 313 Human immunodeficiency virus 1 Fragment: core
Gene Name(s): env
antibody 17b light chain L, Q 214 Homo sapiens Fragment: ANTIGEN-BINDING FRAGMENT, FAB
antibody 17b heavy chain H, R 229 Homo sapiens Fragment: ANTIGEN-BINDING FRAGMENT, FAB
F23, scorpion-toxin mimic of CD4 M, S 27 synthetic

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NDG
Query on NDG

G 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

G, M 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IPA
Query on IPA

G, P ISOPROPYL ALCOHOL
2-PROPANOL (Synonym)
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
MPT
Query on MPT
M, S NON-POLYMER C3 H6 O2 S --
VLM
Query on VLM
M, S L-PEPTIDE LINKING C5 H12 N2 O --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.209
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 51.62 α = 90.00
b = 157.04 β = 93.45
c = 108.93 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-02-25
  • Released Date: 2005-05-03
  • Deposition author(s): Huang, C.C., Stricher, F., Martin, L., Decker, J.M., Majeed, S., Barthe, P., Hendrickson, W.A., Robinson, J., Roumestand, C., Sodroski, J., Wyatt, R., Shaw, G.M., Vita, C., 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