2I60

Crystal structure of [Phe23]M47, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 GP120 envelope glycoprotein and anti-HIV-1 antibody 17B

Structural Biology Knowledgebase: 2I60 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.215

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2I60

Classification: VIRAL PROTEIN / IMMUNE SYSTEM

Total Structure Weight: 174944.23

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
[PHE23]M47, SCORPION-TOXIN MIMIC OF CD4 M, S 27 Synthetic construct

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

G, P 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)
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 3 Unique
ID Chains Type Formula 2D Diagram Parent
MPT
Query on MPT
M, S NON-POLYMER C3 H6 O2 S --
DPR
Query on DPR
M, S D-PEPTIDE LINKING C5 H9 N O2 --
VLM
Query on VLM
M, S L-PEPTIDE LINKING C5 H12 N2 O --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.215
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 51.44 α = 90.00
b = 157.76 β = 93.74
c = 109.85 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-08-26
  • Released Date: 2006-10-10
  • Deposition author(s): Huang, C.-C., Kwong, P.D.

Revision History

  • 2012-06-06
    Type: Function and keywords | Details: Remove virus from header - as this is not an intact virus
  • 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