1FLH | pdb_00001flh

CRYSTAL STRUCTURE OF HUMAN UROPEPSIN AT 2.45 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1FLH/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2000-08-14 Released: 2001-10-31 
• Deposition Author(s): Canduri, F., Teodoro, L.G.V.L., Fadel, V., Lorenzi, C.C.B., Hial, V., Gomes, R.A.S., Neto, J.R., De Azevedo Jr., W.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Work: 
  0.161 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Structure of human uropepsin at 2.45 A resolution.

Canduri, F., Teodoro, L.G., Fadel, V., Lorenzi, C.C., Hial, V., Gomes, R.A., Neto, J.R., de Azevedo, W.F.

(2001) Acta Crystallogr D Biol Crystallogr 57: 1560-1570

• PubMed: 11679720 
• DOI: https://doi.org/10.1107/s0907444901013865
• Primary Citation Related Structures: 
  1FLH


• PubMed Abstract: 
  

  The molecular structure of human uropepsin, an aspartic proteinase from the urine produced in the form of pepsinogen A in the gastric mucosa, has been determined by molecular replacement using human pepsin as the search model. Crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 50.99, b = 75.56, c = 89.90 A. Crystallographic refinement led to an R factor of 0.161 at 2.45 A resolution. The positions of 2437 non-H protein atoms in 326 residues have been determined and the model contains 143 water molecules. The structure is bilobal, consisting of two predominantly beta-sheet lobes which, as observed in other aspartic proteinases, are related by a pseudo-twofold axis. A model of the uropepsin-pepstatin complex has been constructed based on the high-resolution crystal structure of pepsin complexed with pepstatin.

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Organizational Affiliation: 
• Departamento de Física, IBILCE, UNESP, São José do Rio Preto, SP 15054-000, Brazil.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.62 kDa 
• Atom Count: 2,580 
• Modeled Residue Count: 326 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UROPEPSIN	A	326	Homo sapiens	Mutation(s): 0  EC: 3.4.23.1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DJD7 (Homo sapiens) Explore P0DJD7  Go to UniProtKB:  P0DJD7
PHAROS:  P0DJD7 GTEx:  ENSG00000229183

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Work:  0.161 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.989	α = 90
b = 75.557	β = 90
c = 89.896	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-10-31 
Deposition Author(s): Canduri, F., Teodoro, L.G.V.L., Fadel, V., Lorenzi, C.C.B., Hial, V., Gomes, R.A.S., Neto, J.R., De Azevedo Jr., W.F.

Revision History  

• Version 1.0: 2001-10-31
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-09
  Changes: Structure summary