Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 45378.45 
• Atom Count: 3179 
• Residue Count: 380 
• Unique protein chains: 1

1QMU

Duck carboxypeptidase D domain II

• DOI: 10.2210/pdb1QMU/pdb

• Classification: CARBOXYPEPTIDASE
• Organism(s): Lophonetta specularioides
• Expression System: Komagataella pastoris


• Deposited: 1999-10-06 Released: 2000-10-13 
• Deposition Author(s): Gomis-Rueth, F.X., Coll, M., Aviles, F.X., Vendrell, J., Fricker, L.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.236 
• R-Value Work: 0.198 

Literature

Crystal Structure of Avian Carboxypeptidase D Domain II : A Prototype for the Regulatory Metallocarboxypeptidase Subfamily

Gomis-Rueth, F.X., Companys, V., Qian, Y., Fricker, L.D., Vendrell, J., Aviles, F.X., Coll, M.

(1999) Embo J. 18: 5817

• PubMed: 10545093 
• DOI: 10.1093/emboj/18.21.5817
• Also Cited By: 1H8L


• PubMed Abstract: 
  

The crystal structure of domain II of duck carboxypeptidase D, a prohormone/propeptide processing enzyme integrated in a three repeat tandem in the natural system, has been solved, constituting a prototype for members of the regulatory metallocarboxypeptidase subfamily. It displays a 300 residue N-terminal alpha/beta-hydrolase subdomain with overall topological similarity to and general coincidence of the key catalytic residues with the archetypal pancreatic carboxypeptidase A. However, numerous significant insertions/deletions in segments forming the funnel-like access to the active site explain differences in specificity towards larger protein substrates or inhibitors. This alpha/beta-hydrolase subdomain is followed by a C-terminal 80 residue beta-sandwich subdomain, unique for these regulatory metalloenzymes and topologically related to transthyretin and sugar-binding proteins. The structure described here establishes the fundamentals for a better understanding of the mechanism ruling events such as prohormone processing and will enable modelling of regulatory carboxypeptidases as well as a more rational design of inhibitors of carboxypeptidase D.

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Organizational Affiliation: 

Institut de Biologia Molecular de Barcelona, CID-CSIC, Jordi Girona, 18-26, 08034 Barcelona, Spain.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CARBOXYPEPTIDASE GP180 RESIDUES 503-882	A	380	Lophonetta specularioides	Mutation(s): 0  Gene Names: CPD EC: 3.4.17.22
Find proteins for P83852 (Lophonetta specularioides) Go to Gene View: CPD Go to UniProtKB:  P83852

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.236 
• R-Value Work: 0.198 
• Space Group: P 2₁ 3

Unit Cell:

Length (Å)	Angle (°)
a = 135.540	α = 90.00
b = 135.540	β = 90.00
c = 135.540	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
SCALA	data scaling
MOSFLM	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-10-06 
• Released Date: 2000-10-13 
• Deposition Author(s): Gomis-Rueth, F.X., Coll, M., Aviles, F.X., Vendrell, J., Fricker, L.D.

Revision History 

• Version 1.0: 2000-10-13
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2019-07-24
  Type: Data collection, Derived calculations