7YCF

HYDROXYNITRILE LYASE FROM THE MILLIPEDE, Oxidus gracilis IN ACETONITRILE

PDB DOI: https://doi.org/10.2210/pdb7YCF/pdb

Classification: LYASE
Organism(s): Oxidus gracilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-07-01 Released: 2024-01-24
Deposition Author(s): Chaikaew, S., Watanabe, Y., Zheng, D., Motojima, F., Asano, Y.
Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.203
R-Value Work: 0.173

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure-based site-directed mutagenesis of hydroxynitrile lyase from cyanogenic millipede, Oxidus gracilis for enhancing catalytic efficiency and enantioselectivity

Chaikaew, S., Watanabe, Y., Zheng, D., Motojima, F., Asano, Y.

To be published.

Macromolecule Content

Total Structure Weight: 83.9 kDa
Atom Count: 5,594
Modelled Residue Count: 652
Deposited Residue Count: 736
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxynitrile lyase	A, B, C, D	184	Oxidus gracilis	Mutation(s): 0 Gene Names: OgraHNL
UniProt
Find proteins for A0A2Z5XCT7 (Oxidus gracilis) Explore A0A2Z5XCT7 Go to UniProtKB: A0A2Z5XCT7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2Z5XCT7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain Z [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth C]	GA [auth D] J [auth A] K [auth A] L [auth A] Q [auth B] GA [auth D], J [auth A], K [auth A], L [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain GA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Z [auth C] Interactions & Density Focus chain GA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Z [auth C]
CNH (Subject of Investigation/LOI) Query on CNH Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain E [auth A] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] E [auth A] AA [auth D], BA [auth D], CA [auth D], DA [auth D], E [auth A], EA [auth D], F [auth A], G [auth A], H [auth A], M [auth B], N [auth B], O [auth B], U [auth C], V [auth C], W [auth C], X [auth C]	2-HYDROXY-2-METHYLPROPANENITRILE C₄ H₇ N O MWFMGBPGAXYFAR-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain Y [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Y [auth C]	FA [auth D], I [auth A], P [auth B], Y [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain FA [auth D] Focus chain I [auth A] Focus chain P [auth B] Focus chain Y [auth C] Interactions & Density Focus chain FA [auth D] Focus chain I [auth A] Focus chain P [auth B] Focus chain Y [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.203
R-Value Work: 0.173
Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.11	α = 90
b = 123.11	β = 90
c = 129.59	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-01-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJER1102
Japan Society for the Promotion of Science (JSPS)	Japan	17H06169
Japan Society for the Promotion of Science (JSPS)	Japan	22H00361