1E55

Crystal structure of the inactive mutant Monocot (Maize ZMGlu1) beta-glucosidase ZMGluE191D in complex with the competitive inhibitor dhurrin

PDB DOI: https://doi.org/10.2210/pdb1E55/pdb

Classification: HYDROLASE
Organism(s): Zea mays
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2000-07-18 Released: 2000-12-11
Deposition Author(s): Czjzek, M., Cicek, M., Bevan, D.R., Zamboni, V., Henrissat, B., Esen, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.235
R-Value Work: 0.196
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 117.58 kDa
Atom Count: 8,594
Modelled Residue Count: 982
Deposited Residue Count: 1,024
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-GLUCOSIDASE	A, B	512	Zea mays	Mutation(s): 1 EC: 3.2.1.21
UniProt
Find proteins for P49235 (Zea mays) Explore P49235 Go to UniProtKB: P49235
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49235
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
DHR Query on DHR Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	(2S)-HYDROXY(4-HYDROXYPHENYL)ETHANENITRILE C₈ H₇ N O₂ HOOOPXDSCKBLFG-MRVPVSSYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
DHR	Binding MOAD: 1E55	Ki: 7.60e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.235
R-Value Work: 0.196
R-Value Observed: 0.196
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.8	α = 90
b = 95	β = 90
c = 117.5	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2000-12-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2000-12-11
Type: Initial release
Version 1.1: 2015-10-14
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
Version 1.2: 2019-01-16
Changes: Data collection, Database references
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary

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1E55

Crystal structure of the inactive mutant Monocot (Maize ZMGlu1) beta-glucosidase ZMGluE191D in complex with the competitive inhibitor dhurrin

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)