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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.194 (Depositor), 0.197 (DCC)
R-Value Work:
0.178 (Depositor), 0.180 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of Haliotis discus hannai Prolyl Endopeptidase

Li, W., Cao, M.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1X9T5X9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BKO Query on BKO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	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		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.194 (Depositor), 0.197 (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

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Entry History

Deposition Data

Released Date: 2020-02-05

Deposition Author(s):

Revision History (Full details and data files)

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