Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

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

Macromolecule Content

• Total Structure Weight: 70.00 kDa 
• Atom Count: 4971 
• Modelled Residue Count: 587 
• Deposited Residue Count: 607 
• Unique protein chains: 4

1DAN

Complex of active site inhibited human blood coagulation factor VIIA with human recombinant soluble tissue factor

• DOI: 10.2210/pdb1DAN/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Mesocricetus auratus, Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 1997-03-05 Released: 1997-09-04 
• Deposition Author(s): Banner, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.218 
• R-Value Work: 0.187 
• R-Value Observed: 0.187 

Literature

The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor.

Banner, D.W., D'Arcy, A., Chene, C., Winkler, F.K., Guha, A., Konigsberg, W.H., Nemerson, Y., Kirchhofer, D.

(1996) Nature 380: 41-46

• PubMed: 8598903 
• DOI: 10.1038/380041a0
• Primary Citation of Related Structures:  
  1DAN


• PubMed Abstract: 
  

Blood coagulation is initiated when tissue factor binds to coagulation factor VIIa to give an enzymatically active complex which then activates factors IX and X, leading to thrombin generation and clot formation. We have determined the crystal structure at 2.0-A degrees resolution of active-site-inhibited factor VIIa complexed with the cleaved extracellular domain of tissue factor. In the complex, factor VIIa adopts an extended conformation. This structure provides a basis for understanding many molecular aspects of the initiation of coagulation.

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Organizational Affiliation: 

Pharma Division, F. Hoffmann-La Roche, Basle, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BLOOD COAGULATION FACTOR VIIA light chain	A [auth L]	152	Homo sapiens	Mutation(s): 0  Gene Names: F7 EC: 3.4.21.21 Membrane Entity: Yes
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
BLOOD COAGULATION FACTOR VIIA heavy chain	B [auth H]	254	Homo sapiens	Mutation(s): 0  Gene Names: F7 EC: 3.4.21.21 Membrane Entity: Yes
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
SOLUBLE TISSUE FACTOR	C [auth T]	80	Homo sapiens	Mutation(s): 0  Gene Names: F3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P13726 (Homo sapiens) Explore P13726  Go to UniProtKB:  P13726
PHAROS:  P13726 GTEx:  ENSG00000117525

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
SOLUBLE TISSUE FACTOR	D [auth U]	121	Homo sapiens	Mutation(s): 0  Gene Names: F3 Membrane Entity: Yes
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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0Z6 (Subject of Investigation/LOI)	O [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
BGC (Subject of Investigation/LOI)	E [auth L]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
FUC (Subject of Investigation/LOI)	F [auth L]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
CAC	Q [auth H]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
CA	G [auth L],  H [auth L],  I [auth L],  J [auth L],  K [auth L],  L,  M [auth L],  N [auth L],  P [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	R [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CGU	A [auth L]	L-PEPTIDE LINKING	C6 H9 N O6		GLU

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 8
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000369 (0Z6)	O [auth H]	D-Phe-Phe-Arg Chloromethylketone	Peptide-like /  Inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.218 
• R-Value Work: 0.187 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.65	α = 90
b = 82.55	β = 90
c = 126.5	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 1997-03-05 
• Released Date: 1997-09-04 
Deposition Author(s): Banner, D.W.

Revision History  

• Version 1.0: 1997-09-04
  Type: Initial release
  
• Version 1.1: 2008-03-10
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary