5WY9 | pdb_00005wy9

Apo form crystal structure of human Lipocalin PGDS .

• PDB DOI: https://doi.org/10.2210/pdb5WY9/pdb

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


• Deposited: 2017-01-11 Released: 2017-01-25 
• Deposition Author(s): Saif, M., Pervushin, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

To be published

Saif, M., Pervushin, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 20.24 kDa 
• Atom Count: 1,454 
• Modeled Residue Count: 158 
• Deposited Residue Count: 176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin-H2 D-isomerase	A	176	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PG	D [auth A]	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C11 H24 O6 SLNYBUIEAMRFSZ-UHFFFAOYSA-N
PG0	B [auth A], C [auth A]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.27	α = 90
b = 56.5	β = 90
c = 72.529	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data processing
SCALA	data scaling
PHASER	phasing
iMOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-25 
Deposition Author(s): Saif, M., Pervushin, K.

Revision History  

• Version 1.0: 2017-01-25
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Data collection
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description