1DVA | pdb_00001dva

Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor VIIA

• PDB DOI: https://doi.org/10.2210/pdb1DVA/pdb

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


• Deposited: 2000-01-20 Released: 2000-05-12 
• Deposition Author(s): Eigenbrot, C., Ultsch, M.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.295 (Depositor) 
• R-Value Work: 
  0.225 (Depositor) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Peptide exosite inhibitors of factor VIIa as anticoagulants.

Dennis, M.S., Eigenbrot, C., Skelton, N.J., Ultsch, M.H., Santell, L., Dwyer, M.A., O'Connell, M.P., Lazarus, R.A.

(2000) Nature 404: 465-470

• PubMed: 10761907 
• DOI: https://doi.org/10.1038/35006574
• Primary Citation Related Structures: 
  1DVA


• PubMed Abstract: 
  

  Potent anticoagulants have been derived by targeting the tissue factor-factor VIIa complex with naive peptide libraries displayed on M13 phage. The peptides specifically block the activation of factor X with a median inhibitory concentration of 1 nM and selectively inhibit tissue-factor-dependent clotting. The peptides do not bind to the active site of factor VIIa; rather, they work by binding to an exosite on the factor VIIa protease domain, and non-competitively inhibit activation of factor X and amidolytic activity. One such peptide (E-76) has a well defined structure in solution determined by NMR spectroscopy that is similar to the X-ray crystal structure when complexed with factor VIIa. These structural and functional studies indicate an allosteric 'switch' mechanism of inhibition involving an activation loop of factor VIIa and represent a new framework for developing inhibitors of serine proteases.

---

Organizational Affiliation: 
• Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 85.05 kDa 
• Atom Count: 5,917 
• Modeled Residue Count: 748 
• Deposited Residue Count: 750 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DES-GLA FACTOR VIIA (HEAVY CHAIN)	A [auth H], D [auth I]	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DES-GLA FACTOR VIIA (LIGHT CHAIN)	B [auth L], E [auth M]	101	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
PEPTIDE E-76	C [auth X], F [auth Y]	20	N/A	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	G [auth A]	2		O-Glycosylation
Glycosylation Resources
GlyTouCan: G84224TW GlyCosmos: G84224TW GlyGen: G84224TW

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0Z6	H, N [auth I]	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
GLC	Q [auth M]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
FUL	R [auth M]	beta-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-KGJVWPDLSA-N
FUC	K [auth L], L	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
CAC	J [auth H], P [auth I]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
CA	I [auth H], M [auth L], O [auth I], S [auth M]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

2 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000369 (0Z6)	H, N [auth I]	D-Phe-Phe-Arg Chloromethylketone	Peptide-like / Inhibitor

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004	G [auth A]	beta-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.295 (Depositor) 
• R-Value Work:  0.225 (Depositor) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.49	α = 90
b = 55.26	β = 99.48
c = 111.73	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
TRUNCATE	data reduction
AMoRE	phasing
X-PLOR	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-05-12 
Deposition Author(s): Eigenbrot, C., Ultsch, M.H.

Revision History  

• Version 1.0: 2000-05-12
  Type: Initial release
  
• Version 1.1: 2008-01-08
  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 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-10-30
  Changes: Advisory, Data collection, Database references, Structure summary