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 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 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: 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.


  • Organizational Affiliation

    Celera, Inc., 180 Kimball Road, South San Francisco, CA 94080, USA. [email protected]


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine protease hepsin114Homo sapiensMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05981
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serine protease hepsin255Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05981
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CR4
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
Binding Affinity Annotations 
IDSourceBinding 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 = 58.8α = 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
  • Version 1.5: 2023-08-16
    Changes: Data collection, Refinement description
  • Version 1.6: 2024-10-30
    Changes: Structure summary