5YX1

Crystal structure of hematopoietic prostaglandin D synthase in complex with U004

PDB DOI: https://doi.org/10.2210/pdb5YX1/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-12-01 Released: 2018-12-05
Deposition Author(s): Kamo, M., Furubayashi, N., Inaka, K., Aritake, K., Urade, Y., Takaya, D., Tanaka, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.216
R-Value Work: 0.185
R-Value Observed: 0.186

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of hematopoietic prostaglandin D synthase in complex with U004

Inaka, K., Furubayashi, N., Kamo, M., Aritake, K., Urade, Y., Takaya, D., Tanaka, A.

To be published.

Macromolecule Content

Total Structure Weight: 95.76 kDa
Atom Count: 7,634
Modelled Residue Count: 792
Deposited Residue Count: 792
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hematopoietic prostaglandin D synthase	A, B, C, D	198	Homo sapiens	Mutation(s): 0 Gene Names: HPGDS, GSTS, PGDS, PTGDS2 EC: 5.3.99.2 (PDB Primary Data), 2.5.1.18 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O60760 (Homo sapiens) Explore O60760 Go to UniProtKB: O60760
PHAROS: O60760 GTEx: ENSG00000163106
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60760
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UX4 Query on UX4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	H [auth B], L [auth C], N [auth D]	ethyl 4-[(8R)-3,8-dimethyl-4-oxo-4,6,7,8,9,10-hexahydrothieno[2',3':4,5]pyrimido[1,2-a]azepin-2-yl]carbamoylpiperazine-1-carboxylate C₂₁ H₂₉ N₅ O₄ S XBHQVTSPEFNYKC-CYBMUJFWSA-N		Interactions Focus chain H [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain H [auth B] Focus chain L [auth C] Focus chain N [auth D]
GSH Query on GSH Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	F [auth A], G [auth B], K [auth C], M [auth D]	GLUTATHIONE C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain M [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain O [auth D] MOL2 format, chain I [auth B] MOL2 format, chain O [auth D] mmCIF format, chain I [auth B] mmCIF format, chain O [auth D]	I [auth B], O [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain O [auth D] Interactions & Density Focus chain I [auth B] Focus chain O [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth C] mmCIF format, chain E [auth A] mmCIF format, chain J [auth C]	E [auth A], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.216
R-Value Work: 0.185
R-Value Observed: 0.186
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.447	α = 92.2
b = 47.119	β = 98.67
c = 91.924	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-12-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-12-05
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

5YX1

Crystal structure of hematopoietic prostaglandin D synthase in complex with U004

Crystal structure of hematopoietic prostaglandin D synthase in complex with U004

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)