4A94 | pdb_00004a94

Structure of the carboxypeptidase inhibitor from Nerita versicolor in complex with human CPA4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.235 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of a Novel Metallo-Carboxypeptidase Inhibitor from the Marine Mollusk Nerita Versicolor in Complex with Human Carboxypeptidase A4.

Covaleda, G.Alonso Del Rivero, M.Chavez, M.A.Aviles, F.X.Reverter, D.

(2012) J Biological Chem 287: 9250

  • DOI: https://doi.org/10.1074/jbc.M111.330100
  • Primary Citation of Related Structures:  
    4A94

  • PubMed Abstract: 

    NvCI is a novel exogenous proteinaceous inhibitor of metallocarboxypeptidases from the marine snail Nerita versicolor. The complex between human carboxypeptidase A4 and NvCI has been crystallized and determined at 1.7 Å resolution. The NvCI structure defines a distinctive protein fold basically composed of a two-stranded antiparallel β-sheet connected by three loops and the inhibitory C-terminal tail and stabilized by three disulfide bridges. NvCI is a tight-binding inhibitor that interacts with the active site of the enzyme in a substrate-like manner. NvCI displays an extended and novel interface with human carboxypeptidase A4, responsible for inhibitory constants in the picomolar range for some members of the M14A subfamily of carboxypeptidases. This makes NvCI the strongest inhibitor reported so far for this family. The structural homology displayed by the C-terminal tails of different carboxypeptidase inhibitors represents a relevant example of convergent evolution.


  • Organizational Affiliation
    • Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CARBOXYPEPTIDASE A4
A, B
310Homo sapiensMutation(s): 0 
EC: 3.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UI42 (Homo sapiens)
Explore Q9UI42 
Go to UniProtKB:  Q9UI42
PHAROS:  Q9UI42
GTEx:  ENSG00000128510 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UI42
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CARBOXYPEPTIDASE INHIBITOR
C, D
53Nerita versicolorMutation(s): 0 
UniProt
Find proteins for P86912 (Nerita versicolor)
Explore P86912 
Go to UniProtKB:  P86912
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP86912
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
I [auth B]
J [auth B]
K [auth C]
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth C],
L [auth D]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.235 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.22α = 90
b = 71.98β = 108.84
c = 79.84γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2012-02-15
    Changes: Other
  • Version 1.2: 2012-03-28
    Changes: Other
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary