4KTY

Fibrin-stabilizing factor with a bound ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of Active Coagulation Factor XIII Triggered by Calcium Binding: Basis for the Design of Next-Generation Anticoagulants.

Stieler, M.Weber, J.Hils, M.Kolb, P.Heine, A.Buchold, C.Pasternack, R.Klebe, G.

(2013) Angew Chem Int Ed Engl 52: 11930-11934


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor XIII A chainA, B738Homo sapiensMutation(s): 2 
Gene Names: F13AF13A1
EC: 2.3.2.13
Find proteins for P00488 (Homo sapiens)
Explore P00488 
Go to UniProtKB:  P00488
NIH Common Fund Data Resources
PHAROS:  P00488
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide-like ligandC, D9N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
T [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , M [auth A] , Q [auth B] , R [auth B] , 
H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  Q [auth B],  R [auth B],  S [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A], N [auth B], O [auth B], P [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
C, DL-PEPTIDE LINKINGC4 H9 N O2ALA
NLE
Query on NLE
C, DL-PEPTIDE LINKINGC6 H13 N O2LEU
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.761α = 88.14
b = 80.51β = 76.7
c = 102.844γ = 82.01
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-04
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references