6JCI | pdb_00006jci

Crystal structure of Prolyl Endopeptidase from Haliotis discus hannai with SUAM-14746

• PDB DOI: https://doi.org/10.2210/pdb6JCI/pdb

• Classification: HYDROLASE
• Organism(s): Haliotis discus hannai
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-01-28 Released: 2020-02-05 
• Deposition Author(s): Li, W., Cao, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Haliotis discus hannai Prolyl Endopeptidase

Li, W., Cao, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 86.53 kDa 
• Atom Count: 6,127 
• Modeled Residue Count: 704 
• Deposited Residue Count: 758 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prolyl endopeptidase	A	758	Haliotis discus hannai	Mutation(s): 0  Gene Names: PREP EC: 3.4.21
UniProt
Find proteins for A0A1X9T5X9 (Haliotis discus hannai) Explore A0A1X9T5X9  Go to UniProtKB:  A0A1X9T5X9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BKO	D [auth A]	1-[4-oxidanyl-2-(1,3-thiazolidin-3-ylcarbonyl)pyrrolidin-1-yl]-4-[2-[(~{E})-2-phenylethenyl]phenoxy]butan-1-one C26 H30 N2 O4 S VJHGOPMDXSBFHZ-OUKQBFOZSA-N
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.57	α = 90
b = 104.84	β = 90
c = 137.98	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-05 
Deposition Author(s): Li, W., Cao, M.

Revision History  

• Version 1.0: 2020-02-05
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description