6JBY

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.183
R-Value Work: 0.158
R-Value Observed: 0.159

Starting Model: experimental
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This is version 2.2 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O24243
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	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		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.183
R-Value Work: 0.158
R-Value Observed: 0.159
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

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Entry History

Deposition Data

Released Date: 2020-04-01

Deposition Author(s):

Revision History (Full details and data files)

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

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Help and Resources

6JBY

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

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

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)