1J9C

Crystal Structure of tissue factor-factor VIIa complex

• PDB DOI: https://doi.org/10.2210/pdb1J9C/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Cricetulus griseus
• Mutation(s): No 


• Deposited: 2001-05-24 Released: 2004-07-27 
• Deposition Author(s): Huang, M., Ruf, W., Edgington, T.S., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.299 
• R-Value Work: 0.221 

Starting Model: experimental

Literature

Ligand Induced Conformational Transitions of Tissue Factor. Crystal Structure of the Tissue Factor:Factor VIIa Complex.

Huang, M., Ruf, W., Edgington, T.S., Wilson, I.A.

To be published.

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: 63.35 kDa 
• Atom Count: 4,559 
• Modelled Residue Count: 559 
• Deposited Residue Count: 559 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue factor	A [auth T]	210	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P13726 (Homo sapiens) Explore P13726  Go to UniProtKB:  P13726
PHAROS:  P13726 GTEx:  ENSG00000117525

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
factor VIIa light chain	B [auth L]	95	Homo sapiens	Mutation(s): 0  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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P08709-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
factor VIIa heavy chain	C [auth H]	254	Homo sapiens	Mutation(s): 0  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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P08709-1

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
NAG	G [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLC	D [auth L]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
FUL	E [auth L]	beta-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-KGJVWPDLSA-N
CA	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: 2.90 Å
• R-Value Free: 0.299 
• R-Value Work: 0.221 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.038	α = 90
b = 68.302	β = 92.12
c = 78.438	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-07-27 
Deposition Author(s): Huang, M., Ruf, W., Edgington, T.S., Wilson, I.A.

Revision History  

• Version 1.0: 2004-07-27
  Type: Initial release
  
• Version 1.1: 2008-04-27
  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: Data collection, Derived calculations, Structure summary
• Version 1.5: 2023-08-16
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.6: 2024-10-30
  Changes: Structure summary