4Y6D | pdb_00004y6d

Factor Xa complex with GTC000101

• PDB DOI: https://doi.org/10.2210/pdb4Y6D/pdb

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


• Deposited: 2015-02-12 Released: 2015-09-30 
• Deposition Author(s): Convery, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.233 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.199 (Depositor) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

TBA

Convery, M.A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 44.23 kDa 
• Atom Count: 2,623 
• Modeled Residue Count: 282 
• Deposited Residue Count: 388 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X	A	254	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 X	B	134	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
48U	C [auth A]	4-[(3S)-3-({[(E)-2-(5-chlorothiophen-2-yl)ethenyl]sulfonyl}amino)-2-oxopyrrolidin-1-yl]-3-fluoro-N,N-dimethylbenzamide C19 H19 Cl F N3 O4 S2 YVFKLOGRKAMHKF-HQPKTYMTSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
48U	BindingDB:  4Y6D	Ki: 1.5 (nM) from 1 assay(s)
		IC50: 4.83 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.233 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.199 (Depositor) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.863	α = 90
b = 72.729	β = 90
c = 78.586	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-30 
Deposition Author(s): Convery, M.A.

Revision History  

• Version 1.0: 2015-09-30
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary