3O19

Structure-function analysis of human L-Prostaglandin D Synthase bound with fatty acid

PDB DOI: https://doi.org/10.2210/pdb3O19/pdb

Classification: ISOMERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-07-21 Released: 2010-09-22
Deposition Author(s): Zhou, Y., Shaw, N., Li, Y., Zhao, Y., Zhang, R., Liu, Z.-J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.244
R-Value Work: 0.175
R-Value Observed: 0.178

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure-function analysis of human L-Prostaglandin D Synthase bound with fatty acid

Zhou, Y., Shaw, N., Li, Y., Zhao, Y., Zhang, R., Liu, Z.-J.

To be published.

Macromolecule Content

Total Structure Weight: 18.63 kDa
Atom Count: 1,451
Modelled Residue Count: 154
Deposited Residue Count: 162
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin-H2 D-isomerase	A	162	Homo sapiens	Mutation(s): 1 Gene Names: PTGDS, PDS EC: 5.3.99.2
UniProt & NIH Common Fund Data Resources
Find proteins for P41222 (Homo sapiens) Explore P41222 Go to UniProtKB: P41222
PHAROS: P41222 GTEx: ENSG00000107317
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41222
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLA Query on OLA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	OLEIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-KTKRTIGZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.244
R-Value Work: 0.175
R-Value Observed: 0.178
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.512	α = 90
b = 60.512	β = 90
c = 177.23	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-09-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-09-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

3O19

Structure-function analysis of human L-Prostaglandin D Synthase bound with fatty acid

Structure-function analysis of human L-Prostaglandin D Synthase bound with fatty acid

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)