2QPU

Sugar tongs mutant S378P in complex with acarbose

PDB DOI: https://doi.org/10.2210/pdb2QPU/pdb

Classification: HYDROLASE
Organism(s): Hordeum vulgare
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2007-07-25 Released: 2008-07-01
Deposition Author(s): Aghajari, N., Jensen, M.H., Tranier, S., Haser, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.209
R-Value Work: 0.178
R-Value Observed: 0.178

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 137.26 kDa
Atom Count: 11,424
Modelled Residue Count: 1,212
Deposited Residue Count: 1,215
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-amylase type A isozyme	A, B, C	405	Hordeum vulgare	Mutation(s): 2 Gene Names: AMY1.1 EC: 3.2.1.1
UniProt
Find proteins for P00693 (Hordeum vulgare) Explore P00693 Go to UniProtKB: P00693
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00693
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	D	3	N/A	N/A	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G08743RW GlyCosmos: G08743RW

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QPU Query on QPU Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain V [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C]	J [auth A], K [auth A], Q [auth B], V [auth C]	1,5-anhydro-4-O-(4,6-dideoxy-4-{[(1S,2S,3S,4R,5S,6R)-2,3,4,6-tetrahydroxy-5-methylcyclohexyl]amino}-alpha-D-glucopyranosyl)-D-glucitol C₁₉ H₃₅ N O₁₂ NJMZSGBZXMLUCS-JMXNYNASSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain V [auth C] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain V [auth C]
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain W [auth C] MOL2 format, chain W [auth C]	W [auth C]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain W [auth C] Interactions & Density Focus chain W [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain I [auth A]	I [auth A], P [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth B] Interactions & Density Focus chain I [auth A] Focus chain P [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain R [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain S [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain R [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C]	E [auth A] F [auth A] G [auth A] H [auth A] L [auth B] E [auth A], F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], O [auth B], R [auth C], S [auth C], T [auth C], U [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
QPU	PDBBind: 2QPU	Kd: 2.50e+5 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900022 Query on PRD_900022	D	beta-acarbose	Oligosaccharide / Inhibitor		Interactions Focus chain D Interactions & Density Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.209
R-Value Work: 0.178
R-Value Observed: 0.178
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 218.93	α = 90
b = 89.65	β = 90
c = 62.08	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-07-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-07-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2013-03-06
Changes: Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2021-10-20
Changes: Database references, Structure summary
Version 2.2: 2023-08-30
Changes: Data collection, Refinement description

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Help and Resources

2QPU

Sugar tongs mutant S378P in complex with acarbose

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2