5AQ0 | pdb_00005aq0

The structure of the Transthyretin-like domain of the first catalytic domain of the HUMAN Carboxypeptidase D

• PDB DOI: https://doi.org/10.2210/pdb5AQ0/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-09-18 Released: 2016-09-28 
• Deposition Author(s): Gallego, P., Garcia-Pardo, J., Lorenzo, J., Aviles, F.X., Ventura, S., Reverter, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 
  0.175 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

The Structure of the Ttldomain of the Human Carboxypeptidase D

Gallego, P., Garcia-Pardo, J., Berenguer, E., Lorenzo, J., Aviles, F.X., Ventura, S., Reverter, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.61 kDa 
• Atom Count: 1,580 
• Modeled Residue Count: 163 
• Deposited Residue Count: 164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBOXYPEPTIDASE D	A, B	82	Homo sapiens	Mutation(s): 0  EC: 3.4.17.22
UniProt & NIH Common Fund Data Resources
Find proteins for O75976 (Homo sapiens) Explore O75976  Go to UniProtKB:  O75976
PHAROS:  O75976 GTEx:  ENSG00000108582

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free:  0.175 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.773	α = 90
b = 46.051	β = 90.18
c = 42.73	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
CCP4I	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-28 
Deposition Author(s): Gallego, P., Garcia-Pardo, J., Lorenzo, J., Aviles, F.X., Ventura, S., Reverter, D.

Revision History  

• Version 1.0: 2016-09-28
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other