Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 45.29 kDa 
• Atom Count: 3300 
• Modelled Residue Count: 380 
• Deposited Residue Count: 380 
• Unique protein chains: 1

1QMU

Duck carboxypeptidase D domain II

• PDB DOI: 10.2210/pdb1QMU/pdb

• Classification: CARBOXYPEPTIDASE
• Organism(s): Lophonetta specularioides
• Expression System: Komagataella pastoris
• Mutation(s): No 


• 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.236 
• R-Value Work: 0.198 
• R-Value Observed: 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
• Primary Citation of Related Structures:  
  1QMU


• 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.

---

Organizational Affiliation: 

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

Macromolecules

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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.236 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 
• Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.54	α = 90
b = 135.54	β = 90
c = 135.54	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary