6X0S | pdb_00006x0s

Structure of human plasma factor XIIa in complex with (2S)-4-(5-chloro-1,3-benzoxazol-2-yl)-1-(N,3-dicyclohexyl-D-alanyl)-N-[(thiophen-2-yl)methyl]piperazine-2-carboxamide (compound 7)

• PDB DOI: https://doi.org/10.2210/pdb6X0S/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2020-05-17 Released: 2021-05-19 
• Deposition Author(s): Orth, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.251 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Structure of human plasma factor XIIa in complex with (2S)-4-(5-chloro-1,3-benzoxazol-2-yl)-1-(N,3-dicyclohexyl-D-alanyl)-N-[(thiophen-2-yl)methyl]piperazine-2-carboxamide (compound 7)

Rao, A.U., Chu, H.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 85.74 kDa 
• Atom Count: 5,818 
• Modelled Residue Count: 718 
• Deposited Residue Count: 777 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor XII	A, B, C	259	Homo sapiens	Mutation(s): 0  EC: 3.4.21.38
UniProt & NIH Common Fund Data Resources
Find proteins for P00748 (Homo sapiens) Explore P00748  Go to UniProtKB:  P00748
PHAROS:  P00748 GTEx:  ENSG00000131187

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UJA (Subject of Investigation/LOI)	D [auth A], F [auth B], G [auth C]	(2S)-4-(5-chloro-1,3-benzoxazol-2-yl)-1-(N,3-dicyclohexyl-D-alanyl)-N-[(thiophen-2-yl)methyl]piperazine-2-carboxamide C32 H42 Cl N5 O3 S WQMFHHFJPDQBMH-IZLXSDGUSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.251 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.157	α = 90
b = 133.328	β = 104.41
c = 88.915	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
STARANISO	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-19 
Deposition Author(s): Orth, P.

Revision History  

• Version 1.0: 2021-05-19
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary