6JBY | pdb_00006jby

Crystal structure of endo-deglycosylated hydroxynitrile lyase isozyme 5 of Prunus communis

• PDB DOI: https://doi.org/10.2210/pdb6JBY/pdb

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


• Deposited: 2019-01-27 Released: 2020-04-01 
• 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: 
  0.183 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

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 10: 5757-5763

• 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)

Macromolecule Content 

• Total Structure Weight: 61.5 kDa 
• Atom Count: 4,827 
• Modeled Residue Count: 521 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hnl isoenzyme 5	A	542	Prunus dulcis	Mutation(s): 0  Gene Names: hnl5 EC: 4.1.2.10
UniProt
Find proteins for O24243 (Prunus dulcis) Explore O24243  Go to UniProtKB:  O24243
Glycosylation
Glycosylation Sites: 6

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	H [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAG	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.183 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.525	α = 90
b = 91.307	β = 90
c = 132.018	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-01 
Deposition Author(s): Zheng, Y.C., Li, F.L., Yu, H.L., Xu, J.H.

Revision History  

• Version 1.0: 2020-04-01
  Type: Initial release
  
• Version 1.1: 2020-05-13
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-30
  Changes: Structure summary
• Version 2.3: 2025-03-05
  Changes: Database references