4YGB

Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-free form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Interaction mode of coagulation factors V and VIII with the cargo receptor MCFD2/ERGIC-53 complex

Satoh, T.Nishio, M.Yagi-Utsumi, M.Suzuki, K.Anzai, T.Mizushima, T.Kamiya, Y.Kato, K.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein ERGIC-53
A, C
246Homo sapiensMutation(s): 0 
Gene Names: LMAN1 (ERGIC53, F5F8D)
Find proteins for P49257 (Homo sapiens)
Go to Gene View: LMAN1
Go to UniProtKB:  P49257
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Multiple coagulation factor deficiency protein 2
B, D
104Homo sapiensMutation(s): 0 
Gene Names: MCFD2 (SDNSF)
Find proteins for Q8NI22 (Homo sapiens)
Go to Gene View: MCFD2
Go to UniProtKB:  Q8NI22
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
B, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.924α = 90.00
b = 116.930β = 120.13
c = 58.065γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPS KAKENHIJapan25121730, 25102008, 24249002
Okazaki ORION project, Ministry of Education, Culture, Sports, Science and TechnologyJapan--
Nanotechnology Platform Project, Ministry of Education, Culture, Sports, Science and TechnologyJapan--

Revision History 

  • Version 1.0: 2016-04-06
    Type: Initial release