4Y7B | pdb_00004y7b

Factor Xa complex with GTC000441

• PDB DOI: https://doi.org/10.2210/pdb4Y7B/pdb

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


• Deposited: 2015-02-13 Released: 2015-09-30 
• Deposition Author(s): Convery, M.A., Young, R.J., Senger, S., Hamblin, J.N., Chan, C., Toomey, J.R., Watson, N.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Factor Xa complex with GTC000441

Convery, M.A., Young, R.J., Senger, S., Hamblin, J.N., Chan, C., Toomey, J.R., Watson, N.S.

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: 44.36 kDa 
• Atom Count: 2,622 
• Modeled Residue Count: 287 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
44I	D [auth A]	6-chloro-N-{(3S)-1-[(2S)-1-{(1R,5S)-7-[2-(methylamino)ethyl]-3,7-diazabicyclo[3.3.1]non-3-yl}-1-oxopropan-2-yl]-2-oxopy rrolidin-3-yl}naphthalene-2-sulfonamide C27 H36 Cl N5 O4 S NSTQUPKYMBYQSS-KSYXXAMZSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.742	α = 90
b = 72.635	β = 90
c = 79.862	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-30 
Deposition Author(s): Convery, M.A., Young, R.J., Senger, S., Hamblin, J.N., Chan, C., Toomey, J.R., Watson, N.S.

Revision History  

• Version 1.0: 2015-09-30
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.2: 2024-10-23
  Changes: Structure summary