6LQY

Crystal complex of endo-deglycosylated hydroxynitrile lyase isozyme 5 of Prunus communis with benzaldehyde

• PDB DOI: https://doi.org/10.2210/pdb6LQY/pdb

• Classification: LYASE
• Organism(s): Prunus dulcis
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2020-01-15 Released: 2020-05-13 
• Deposition Author(s): Zheng, Y.C., Li, F.L., Yu, H.L., Xu, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.189 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Literature

Structure-Guided Tuning of a Hydroxynitrile Lyase to Accept Rigid Pharmaco Aldehydes.

Zheng, Y.C., Li, F.L., Lin, Z.M., Lin, G.Q., Hong, R., Yu, H.L., Xu, J.H.

(2020) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.0c01103

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: 61.23 kDa 
• Atom Count: 4,685 
• Modelled Residue Count: 517 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PREDICTED: (R)-mandelonitrile lyase	A	538	Prunus dulcis	Mutation(s): 0  Gene Names: ALMOND_2B028509
UniProt
Find proteins for O24243 (Prunus dulcis) Explore O24243  Go to UniProtKB:  O24243

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	I [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAG	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
HBX	J [auth A]	benzaldehyde C7 H6 O HUMNYLRZRPPJDN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.189 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.564	α = 90
b = 91.463	β = 90
c = 130.844	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-13 
Deposition Author(s): Zheng, Y.C., Li, F.L., Yu, H.L., Xu, J.H.

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description, Structure summary