5PB1

Crystal Structure of Factor VIIa in complex with benzenecarboximidamide

• PDB DOI: https://doi.org/10.2210/pdb5PB1/pdb
• Deposition Group: G_1002015 ExploreG_1002015

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


• Deposited: 2016-11-10 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: 0.210 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 

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: 36.21 kDa 
• Atom Count: 2,917 
• Modelled Residue Count: 306 
• 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) 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 D]	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) Go to UniProtKB:  P08709
PHAROS:  P08709 GTEx:  ENSG00000057593

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEN	M [auth D]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
SO4	C [auth A], G [auth D], H [auth D], I [auth D], J [auth D], N [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A], K [auth D], L [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	F [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MHO	B [auth D]	L-PEPTIDE LINKING	C5 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.210 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.676	α = 90
b = 95.676	β = 90
c = 117.961	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
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 2.0: 2021-08-18
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2021-11-17
  Changes: Structure summary
• Version 2.2: 2024-04-03
  Changes: Data collection, Refinement description