4Z6A

Crystal Structure of a FVIIa-Trypsin Chimera (YT) in Complex with Soluble Tissue Factor

• PDB DOI: https://doi.org/10.2210/pdb4Z6A/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus, Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-04-04 Released: 2015-12-30 
• Deposition Author(s): Sorensen, A.B., Svensson, L.A., Gandhi, P.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.240 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 62.62 kDa 
• Atom Count: 4,491 
• Modelled Residue Count: 544 
• Deposited Residue Count: 552 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	A [auth L]	96	Homo sapiens	Mutation(s): 0  Gene Names: F7 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709  Go to UniProtKB:  P08709
PHAROS:  P08709 GTEx:  ENSG00000057593

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	B [auth H]	249	Homo sapiens	Mutation(s): 7  Gene Names: F7 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709  Go to UniProtKB:  P08709
PHAROS:  P08709 GTEx:  ENSG00000057593

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue factor	C [auth T]	207	Homo sapiens	Mutation(s): 0  Gene Names: F3
UniProt & NIH Common Fund Data Resources
Find proteins for P13726 (Homo sapiens) Explore P13726  Go to UniProtKB:  P13726
PHAROS:  P13726 GTEx:  ENSG00000117525

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0Z6	F [auth H]	D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-phenylalaninamide C25 H36 Cl N6 O3 ZKHBINZTIMXMQW-CLAROIROSA-O
CIT	H [auth T]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
BGC	D [auth L]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
FUC	E [auth L]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
CA	G [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 6
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000369 (0Z6)	F [auth H]	D-Phe-Phe-Arg Chloromethylketone	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.240 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.03	α = 90
b = 81.7	β = 90
c = 124.56	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-30 
Deposition Author(s): Sorensen, A.B., Svensson, L.A., Gandhi, P.S.

Revision History  

• Version 1.0: 2015-12-30
  Type: Initial release
  
• Version 1.1: 2016-01-13
  Changes: Database references
• Version 1.2: 2016-03-09
  Changes: Database references
• Version 1.3: 2016-12-21
  Changes: Non-polymer description
• Version 1.4: 2018-01-17
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary