1IQF

Human coagulation factor Xa in complex with M55165

• PDB DOI: https://doi.org/10.2210/pdb1IQF/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2001-07-23 Released: 2003-09-23 
• Deposition Author(s): Shiromizu, I., Matsusue, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.277 
• R-Value Work: 0.169 

Literature

Factor Xa Specific Inhibitor that Induces the Novel Binding Model in Complex with Human Fxa

Matsusue, T., Shiromizu, I., Okamoto, A., Nakayama, K., Nishida, H., Mukaihira, T., Miyazaki, Y., Saitou, F., Morishita, H., Ohnishi, S., Mochizuki, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.75 kDa 
• Atom Count: 2,279 
• Modelled Residue Count: 286 
• Deposited Residue Count: 331 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
coagulation Factor Xa	A	235	Homo sapiens	Mutation(s): 0  EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
PHAROS:  P00742 GTEx:  ENSG00000126218

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
coagulation Factor Xa	B [auth L]	96	Homo sapiens	Mutation(s): 0  EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
PHAROS:  P00742 GTEx:  ENSG00000126218

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XMD	D [auth A]	(2R)-4-[(6-CHLORO-2-NAPHTHALENYL)SULFONYL]-6-OXO-1-[[1-(4-PYRIDINYL)-4-PIPERIDINYL]METHYL]-2-PIPERAZINECARBOXYLIC ACID ETHYL ESTER C28 H31 Cl N4 O5 S BVVKZWAFUVRXPJ-AREMUKBSSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.277 
• R-Value Work: 0.169 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.29	α = 90
b = 78.04	β = 90
c = 56.63	γ = 90

Software Package:

Software Name	Purpose
GLRF	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-23 
Deposition Author(s): Shiromizu, I., Matsusue, T.

Revision History  

• Version 1.0: 2003-09-23
  Type: Initial release
  
• Version 1.1: 2007-11-21
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Structure summary