4HAT

Crystal structure of CRM1 inhibitor Leptomycin B in complex with CRM1-Ran-RanBP1

Structural Biology Knowledgebase: 4HAT SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.173
  • R-Value Work: 0.136

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4HAT

Classification: PROTEIN TRANSPORT / ANTIBIOTIC

Total Structure Weight: 159838.48

Macromolecule Entities
Molecule Chains Length Organism Details
GTP-binding nuclear protein Ran A 216 Homo sapiens Gene Name(s): RAN Gene View ARA24 OK/SW-cl.81
Ran-specific GTPase-activating protein 1 B 140 Saccharomyces cerevisiae Fragment: RanDB1 (UNP residues 62-201)
Mutation: A98K
Gene Name(s): YRB1 CST20 HTN1 Gene View SFO1 YDR002W YD8119.08
Exportin-1 C 1023 Saccharomyces cerevisiae Fragment: SEE REMARK 999
Mutation: S205A, T539C, Y1022C
Gene Name(s): CRM1 KAP124 XPO1 Gene View YGR218W G8514

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
LMB
Query on LMB

C Leptomycin B, bound form
C33 H52 O7
GCBBLAVMGONVHO-XYERBDPFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GNP
Query on GNP

A PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

C GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

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

C CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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: 1.78 Å
  • R-Value Free: 0.173
  • R-Value Work: 0.136
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 105.68 α = 90.00
b = 105.68 β = 90.00
c = 305.51 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-27
  • Released Date: 2013-01-09
  • Deposition author(s): Sun, Q., Chook, Y.M.

Revision History

  • 2013-02-06
    Type: Citation | Details: Citation update
  • 2013-01-23
    Type: Citation | Details: Citation update