5SJH | pdb_00005sjh

Crystal Structure of human phosphodiesterase 10

PDB DOI: https://doi.org/10.2210/pdb5SJH/pdb
Deposition Group: G_1002229 | Explore G_1002229

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-02-01 Released: 2022-10-12
Deposition Author(s): Joseph, C., Benz, J., Flohr, A., Rudolph, M.G.
Funding Organization(s): F. Hoffmann-La Roche

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.204 (Depositor), 0.210 (DCC)
R-Value Work:
0.177 (Depositor)
R-Value Observed:
0.179 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Validation slider image for 5SJH

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

Literature

Crystal Structure of a human phosphodiesterase 10 complex

Flohr, A., Schlatter, D., Kuhn, B., Rudolph, M.G.

To be published.

Macromolecule Content

Total Structure Weight: 157.71 kDa
Atom Count: 11,045
Modeled Residue Count: 1,243
Deposited Residue Count: 1,372
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A	A, B, C, D	343	Homo sapiens	Mutation(s): 0 Gene Names: PDE10A EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y233 (Homo sapiens) Explore Q9Y233 Go to UniProtKB: Q9Y233
PHAROS: Q9Y233 GTEx: ENSG00000112541
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y233
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.204 (Depositor), 0.210 (DCC)
R-Value Work: 0.177 (Depositor)
R-Value Observed: 0.179 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.308	α = 90
b = 136.308	β = 90
c = 235.947	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
PHASER	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-10-12

Deposition Author(s):

Funding Organization	Location	Grant Number
F. Hoffmann-La Roche	Switzerland	--

Revision History (Full details and data files)

Version 1.0: 2022-10-12
Type: Initial release
Version 1.1: 2024-04-03
Changes: Data collection, Refinement description

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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.