3TH3

Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors At Physiological Ca2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors At Physiological Ca2+

Vadivel, K.Agah, S.Messer, A.Cascio, D.Bajaj, M.S.Krishnaswamy, S.Esmon, C.T.Padmanabhan, K.Bajaj, S.P.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor VII light chain
L
142Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Go to Gene View: F7
Go to UniProtKB:  P08709
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor VII heavy chain
H
254Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Go to Gene View: F7
Go to UniProtKB:  P08709
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Tissue factor
T
205Homo sapiensMutation(s): 0 
Gene Names: F3
Find proteins for P13726 (Homo sapiens)
Go to Gene View: F3
Go to UniProtKB:  P13726
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0GE
Query on 0GE

Download SDF File 
Download CCD File 
H
N-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-alpha-glutamyl-N-[(2S,3S)-6-carbamimidamido-1-chloro-2-hydroxyhexan-3-yl]glycinamide
1,5-DANSYL-GLU-GLY-ARG-CHLOROMETHYL KETONE, bound form
C26 H38 Cl N7 O7 S
AKFRXQNHCCSRJN-IRFCIJBXSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
H, L
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

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Download CCD File 
T
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
L
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000287 (0GE)
Query on PRD_000287
Hdansyl-Glu-Gly-Arg chloromethyl ketonePeptide-like / Inhibitor

--

Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CGU
Query on CGU
L
L-PEPTIDE LINKINGC6 H9 N O6GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 78.079α = 90.00
b = 68.894β = 91.19
c = 79.153γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
ADSCdata collection
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Other
  • Version 1.2: 2018-01-24
    Type: Database references