4DXA

Co-crystal structure of Rap1 in complex with KRIT1

Structural Biology Knowledgebase: 4DXA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.196

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DXA

Classification: PROTEIN BINDING

Total Structure Weight: 57143.05

Macromolecule Entities
Molecule Chains Length Organism Details
Ras-related protein Rap-1b A 169 Homo sapiens EC#: 3.6.5.2 IUBMB
Mutation: G12V
Gene Name(s): RAP1B Gene View OK/SW-cl.11
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Krev interaction trapped protein 1 B 322 Homo sapiens Fragment: FERM domain
Gene Name(s): KRIT1 Gene View CCM1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
C10 H16 N5 O13 P3 S
XOFLBQFBSOEHOG-UUOKFMHZSA-N
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: 1.95 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.196
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 57.55 α = 90.00
b = 77.97 β = 90.93
c = 59.76 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-27
  • Released Date: 2012-05-16
  • Deposition author(s): Li, X., Zhang, R., Boggon, T.J.

Revision History

  • 2012-07-25
    Type: Citation | Details: Citation update
  • 2012-05-23
    Type: Citation | Details: Citation update