4KTY

Fibrin-stabilizing factor with a bound ligand

• PDB DOI: https://doi.org/10.2210/pdb4KTY/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2013-05-21 Released: 2013-12-04 
• Deposition Author(s): Stieler, M., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

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

• PubMed: 24115223 
• DOI: https://doi.org/10.1002/anie.201305133
• Primary Citation of Related Structures:  
  4KTY

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Organizational Affiliation: 

Department of Pharmaceutical Chemistry, Philipps-University, Marbacher Weg 6, 35032 Marburg (Germany).

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 171.65 kDa 
• Atom Count: 12,087 
• Modelled Residue Count: 1,411 
• Deposited Residue Count: 1,494 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor XIII A chain	A, B	738	Homo sapiens	Mutation(s): 2  Gene Names: F13A, F13A1 EC: 2.3.2.13
UniProt & NIH Common Fund Data Resources
Find proteins for P00488 (Homo sapiens) Explore P00488  Go to UniProtKB:  P00488
PHAROS:  P00488 GTEx:  ENSG00000124491

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide-like ligand	C, D	9	N/A	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	T [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	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
CA	E [auth A], F [auth A], G [auth A], N [auth B], O [auth B], P [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA	C, D	L-PEPTIDE LINKING	C4 H9 N O2		ALA
NLE	C, D	L-PEPTIDE LINKING	C6 H13 N O2		LEU

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001125	C, D	N-[(2S)-2-({(2S)-2-[(N-acetyl-D-alpha-aspartyl)amino]-7-methoxy-7-oxoheptanoyl}amino)butanoyl]-L-norleucyl-L-leucyl-L-prolyl-L-tryptophyl-L-proline	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.761	α = 88.14
b = 80.51	β = 76.7
c = 102.844	γ = 82.01

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-04 
Deposition Author(s): Stieler, M., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2013-12-04
  Type: Initial release
  
• Version 1.1: 2014-03-12
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations