6COE

AtHNL enantioselectivity mutant At-A9-H7 Apo Y13C,Y121L,P126F,L128W,C131T,F179L,A209I with benzaldehyde, MANDELIC ACID NITRILE

PDB DOI: https://doi.org/10.2210/pdb6COE/pdb

Classification: LYASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-03-12 Released: 2019-03-20
Deposition Author(s): Jones, B.J., Kazlauskas, R.J., Desrouleaux, R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 ?
R-Value Free: 0.199
R-Value Work: 0.154
R-Value Observed: 0.156

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

AtHNL enantioselectivity mutants

Jones, B.J., Desrouleaux, R., Kazlauskas, R.J.

To be published.

Macromolecule Content

Total Structure Weight: 60.07 kDa
Atom Count: 4,614
Modelled Residue Count: 517
Deposited Residue Count: 520
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-hydroxynitrile lyase	A, B	260	Arabidopsis thaliana	Mutation(s): 7 Gene Names: HNL, MES5, At5g10300, F18D22_70 EC: 4.1.2.10
UniProt
Find proteins for Q9LFT6 (Arabidopsis thaliana) Explore Q9LFT6 Go to UniProtKB: Q9LFT6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9LFT6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MXN (Subject of Investigation/LOI) Query on MXN Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B]	I [auth A], N [auth B]	(2R)-hydroxy(phenyl)ethanenitrile C₈ H₇ N O NNICRUQPODTGRU-QMMMGPOBSA-N		Interactions Focus chain I [auth A] Focus chain N [auth B] Interactions & Density Focus chain I [auth A] Focus chain N [auth B]
MNN (Subject of Investigation/LOI) Query on MNN Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	H [auth A], M [auth B]	(S)-MANDELIC ACID NITRILE C₈ H₇ N O NNICRUQPODTGRU-MRVPVSSYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain H [auth A] Focus chain M [auth B]
HBX (Subject of Investigation/LOI) Query on HBX Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	benzaldehyde C₇ H₆ O HUMNYLRZRPPJDN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
GOL Query on GOL 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 J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	C [auth A], D [auth A], E [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B]	F [auth A], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 ?
R-Value Free: 0.199
R-Value Work: 0.154
R-Value Observed: 0.156
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 50.024	α = 90
b = 87.231	β = 90
c = 123.283	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-03-20

Deposition Author(s):

Jones, B.J.

Kazlauskas, R.J.

Desrouleaux, R.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM102205

Revision History (Full details and data files)

Version 1.0: 2019-03-20
Type: Initial release
Version 1.1: 2019-04-10
Changes: Author supporting evidence, Data collection
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description

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Help and Resources

6COE

AtHNL enantioselectivity mutant At-A9-H7 Apo Y13C,Y121L,P126F,L128W,C131T,F179L,A209I with benzaldehyde, MANDELIC ACID NITRILE

AtHNL enantioselectivity mutants

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)