1P57

Extracellular domain of human hepsin

• PDB DOI: https://doi.org/10.2210/pdb1P57/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2003-04-25 Released: 2004-01-20 
• Deposition Author(s): Somoza, J.R., Ho, J.D., Luong, C., Sprengeler, P.A., Mortara, K., Shrader, W.D., Sperandio, D., Chan, H., McGrath, M.E., Katz, B.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.206 
• R-Value Work: 0.186 
• R-Value Observed: 0.186 

Starting Model: experimental

Literature

The Structure of the Extracellular Region of Human Hepsin Reveals a Serine Protease Domain and a Novel Scavenger Receptor Cysteine-Rich (SRCR) Domain

Somoza, J.R., Ho, J.D., Luong, C., Ghate, M., Sprengeler, P.A., Mortara, K., Shrader, W.D., Sperandio, D., Chan, H., McGrath, M.E., Katz, B.A.

(2003) Structure 11: 1123-1131

• PubMed: 12962630 
• DOI: https://doi.org/10.1016/s0969-2126(03)00148-5
• Primary Citation of Related Structures:  
  1P57


• PubMed Abstract: 
  

  Hepsin is an integral membrane protein that may participate in cell growth and in maintaining proper cell morphology and is overexpressed in a number of primary tumors. We have determined the 1.75 A resolution structure of the extracellular component of human hepsin. This structure includes a 255-residue trypsin-like serine protease domain and a 109-residue region that forms a novel, poorly conserved, scavenger receptor cysteine-rich (SRCR) domain. The two domains are associated with each other through a single disulfide bond and an extensive network of noncovalent interactions. The structure suggests how the extracellular region of hepsin may be positioned with respect to the plasma membrane.

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Organizational Affiliation: 

Celera, Inc., 180 Kimball Road, South San Francisco, CA 94080, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.35 kDa 
• Atom Count: 3,049 
• Modelled Residue Count: 357 
• Deposited Residue Count: 369 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease hepsin	A	114	Homo sapiens	Mutation(s): 1  EC: 3.4.21 (PDB Primary Data), 3.4.21.106 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P05981 (Homo sapiens) Explore P05981  Go to UniProtKB:  P05981
PHAROS:  P05981 GTEx:  ENSG00000105707

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease hepsin	B	255	Homo sapiens	Mutation(s): 0  EC: 3.4.21 (PDB Primary Data), 3.4.21.106 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P05981 (Homo sapiens) Explore P05981  Go to UniProtKB:  P05981
PHAROS:  P05981 GTEx:  ENSG00000105707

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CR4	C [auth B]	2-{5-[AMINO(IMINIO)METHYL]-1H-BENZIMIDAZOL-2-YL}BENZENOLATE C14 H12 N4 O URJKRCBBKTXOHS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CR4	PDBBind:  1P57	Ki: 4.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.206 
• R-Value Work: 0.186 
• R-Value Observed: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.8	α = 90
b = 47.8	β = 104.8
c = 63.1	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: 2004-01-20 
Deposition Author(s): Somoza, J.R., Ho, J.D., Luong, C., Sprengeler, P.A., Mortara, K., Shrader, W.D., Sperandio, D., Chan, H., McGrath, M.E., Katz, B.A.

Revision History  

• Version 1.0: 2004-01-20
  Type: Initial release
  
• Version 1.1: 2007-10-21
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2016-07-27
  Changes: Derived calculations, Structure summary
• Version 1.4: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.5: 2023-08-16
  Changes: Data collection, Refinement description
• Version 1.6: 2024-10-30
  Changes: Structure summary