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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.95 Å
R-Value Free:
0.175 (Depositor), 0.175 (DCC)
R-Value Work:
0.153 (Depositor), 0.152 (DCC)
R-Value Observed:
0.154 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5AQ0

This is version 1.1 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75976
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.95 Å
R-Value Free: 0.175 (Depositor), 0.175 (DCC)
R-Value Work: 0.153 (Depositor), 0.152 (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

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Entry History

Deposition Data

Released Date: 2016-09-28

Deposition Author(s):

Garcia-Pardo, J.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.