5MHO | pdb_00005mho

FXIIIa in complex with the inhibitor ZED2369

• PDB DOI: https://doi.org/10.2210/pdb5MHO/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2016-11-24 Released: 2017-12-20 
• Deposition Author(s): Stieler, M., Heine, A., Klebe, G.
• Funding Organization(s): BMBF

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

FXIIIa in complex with the inhibitor ZED2369

Stieler, M., Heine, A., Klebe, G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 171.04 kDa 
• Atom Count: 10,661 
• Modeled Residue Count: 1,371 
• 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: F13A1, F13A 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
inhibitor ZED2369	C [auth G], D [auth H]	9	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	H [auth A], L [auth B], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.555	α = 88.2
b = 80.508	β = 76.91
c = 102.904	γ = 82.23

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Stieler, M., Heine, A., Klebe, G.

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Funding Organization	Location	Grant Number
BMBF	Germany	FKZ0316030

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2024-01-17
  Changes: Refinement description
• Version 2.2: 2024-10-09
  Changes: Structure summary