5PB3

Crystal Structure of Factor VIIa in complex with 1-[[3-[4-(5-amino-1H-pyrrolo[3,2-b]pyridin-2-yl)-5-hydroxypyrazol-1-yl]phenyl]methyl]-3-phenylurea

• PDB DOI: https://doi.org/10.2210/pdb5PB3/pdb
• Deposition Group: G_1002016 ExploreG_1002016

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


• Deposited: 2016-11-16 Released: 2017-06-21 
• Deposition Author(s): Stihle, M., Mayweg, A., Roever, S., Rudolph, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.211 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 

Starting Model: other

Literature

Crystal Structure of a Factor VIIa complex

Mayweg, A., Roever, S., Rudolph, M.G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.14 kDa 
• Atom Count: 2,885 
• Modelled Residue Count: 308 
• Deposited Residue Count: 318 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII light chain	A	64	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 heavy chain	B [auth C]	254	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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9S1	F [auth C]	N-({3-[4-(5-amino-1H-pyrrolo[3,2-b]pyridin-2-yl)-5-hydroxy-1H-pyrazol-1-yl]phenyl}methyl)-N'-phenylurea C24 H21 N7 O2 UTXKUUYFKOVOOK-UHFFFAOYSA-N
SO4	C [auth A], K [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A], L [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	G [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	H [auth C], I [auth C], J [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.211 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.192	α = 90
b = 95.192	β = 90
c = 116.08	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Stihle, M., Mayweg, A., Roever, S., Rudolph, M.G.

Revision History  

• Version 1.0: 2017-06-21
  Type: Initial release
  
• Version 1.1: 2018-02-21
  Changes: Structure summary
• Version 1.2: 2021-11-17
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-04-03
  Changes: Data collection, Refinement description