4I1O

Crystal structure of the Legionella pneumophila GAP domain of LepB in complex with Rab1b bound to GDP and BeF3

Structural Biology Knowledgebase: 4I1O SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.217

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4I1O

Classification: PROTEIN TRANSPORT / HYDROLASE

Total Structure Weight: 221229.18

Macromolecule Entities
Molecule Chains Length Organism Details
Ras-related protein Rab-1B A, C, E, G 181 Homo sapiens Fragment: UNP residues 3-174
Gene Name(s): RAB1B Gene View
LepB B, D, F, H 302 Legionella pneumophila Fragment: GAP domain (UNP residues 317-618)
Mutation: K457A, E458A, K460A
Gene Name(s): lepB lpg2490

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GDP
Query on GDP

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

A, C, D, G DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BEF
Query on BEF

A, C, E, G BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, C, E, G 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: 0.249
  • R-Value Work: 0.217
  • Space Group: P 31
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 124.41 α = 90.00
b = 124.41 β = 90.00
c = 147.47 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-11-21
  • Released Date: 2013-01-16
  • Deposition author(s): Gazdag, E.M., Streller, A., Vetter, I.R., Goody, R.S., Itzen, A.

Revision History

  • 2013-02-20
    Type: Citation | Details: Citation update