1P57

Extracellular domain of human hepsin


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 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

    Celera, Inc., 180 Kimball Road, South San Francisco, CA 94080, USA. john.somoza@celera.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine protease hepsinA114Homo sapiensMutation(s): 1 
Gene Names: HPNTMPRSS1
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Serine protease hepsinB255Homo sapiensMutation(s): 0 
Gene Names: HPNTMPRSS1
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CR4 (Subject of Investigation/LOI)
Query on CR4

Download Ideal Coordinates CCD File 
C [auth B]2-{5-[AMINO(IMINIO)METHYL]-1H-BENZIMIDAZOL-2-YL}BENZENOLATE
C14 H12 N4 O
URJKRCBBKTXOHS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CR4 Binding MOAD:  1P57 Ki: 4.00e+4 (nM) from 1 assay(s)
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 = 58.8α = 90
b = 47.8β = 104.8
c = 63.1γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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