1XD2

Crystal Structure of a ternary Ras:SOS:Ras*GDP complex

Structural Biology Knowledgebase: 1XD2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.212

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1XD2

Classification: SIGNALING PROTEIN

Total Structure Weight: 95294.59

Macromolecule Entities
Molecule Chains Length Organism Details
Transforming protein p21/H-Ras-1 A 166 Homo sapiens Fragment: residues 1-166
Mutation: Y64A
Gene Name(s): HRAS Gene View HRAS1
Transforming protein p21/H-Ras-1 B 166 Homo sapiens Fragment: residues 1-166
Gene Name(s): HRAS Gene View HRAS1
Son of sevenless protein homolog 1 C 484 Homo sapiens Fragment: residues 566-1049, including Ras guanine nucleotide exchange factor fragment
Gene Name(s): SOS1 Gene View

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

A GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B, C PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.212
  • Space Group: I 4 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 183.70 α = 90.00
b = 183.70 β = 90.00
c = 177.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-09-03
  • Released Date: 2004-11-02
  • Deposition author(s): Sondermann, H., Soisson, S.M., Boykevisch, S., Yang, S.S., Bar-Sagi, D., Kuriyan, J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4