3A6P

Crystal structure of Exportin-5:RanGTP:pre-miRNA complex

Structural Biology Knowledgebase: 3A6P SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.312
  • R-Value Work: 0.247

Literature

Macromolecules
Sequence Display for 3A6P

Classification: PROTEIN TRANSPORT / NUCLEAR PROTEIN / RNA

Total Structure Weight: 355864.13


Macromolecule Entities
Molecule Chains Length Organism Details
Exportin-5 A, F 1204 Homo sapiens Gene Name(s): XPO5 Gene View KIAA1291 RANBP21
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
13-mer peptide B, G 13 Homo sapiens
GTP-binding nuclear protein Ran C, H 216 Canis lupus EC#: 2.1.1.64 IUBMB
Gene Name(s): RAN Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
pre-microRNA D, I 24 synthetic
pre-microRNA E, J 24 synthetic

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

C, H GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

C, H MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
UNK
Query on UNK
B, G L-PEPTIDE LINKING C4 H9 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.312
  • R-Value Work: 0.247
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 71.16 α = 90.00
b = 304.67 β = 110.79
c = 89.23 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-09-07
  • Released Date: 2009-12-08
  • Deposition author(s): Okada, C., Yamashita, E., Lee, S.J., Shibata, S., Katahira, J., Nakagawa, A., Yoneda, Y., Tsukihara, T.

Revision History

  • 2012-04-25
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4