4IIC

Crystal structure of beta-glucosidase 1 from Aspergillus aculeatus in complex with isofagomine

PDB DOI: https://doi.org/10.2210/pdb4IIC/pdb

Classification: HYDROLASE
Organism(s): Aspergillus aculeatus
Expression System: Aspergillus oryzae
Mutation(s): No

Deposited: 2012-12-20 Released: 2013-04-10
Deposition Author(s): Suzuki, K., Sumitani, J., Kawaguchi, T., Fushinobu, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.184
R-Value Work: 0.145
R-Value Observed: 0.147

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 198.83 kDa
Atom Count: 15,282
Modelled Residue Count: 1,665
Deposited Residue Count: 1,682
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase 1	A, B	841	Aspergillus aculeatus	Mutation(s): 0 Gene Names: bgl1 EC: 3.2.1.21
UniProt
Find proteins for P48825 (Aspergillus aculeatus) Explore P48825 Go to UniProtKB: P48825
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48825
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, G, L, N	3		N-Glycosylation	Interactions Focus chain D Focus chain G Focus chain L Focus chain N Interactions & Density Focus chain D Focus chain G Focus chain L Focus chain N
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, M	10		N-Glycosylation	Interactions Focus chain F Focus chain M Interactions & Density Focus chain F Focus chain M
Glycosylation Resources
GlyTouCan: G89864BN GlyCosmos: G89864BN GlyGen: G89864BN

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, O	7		N-Glycosylation	Interactions Focus chain H Focus chain O Interactions & Density Focus chain H Focus chain O
Glycosylation Resources
GlyTouCan: G92805XC GlyCosmos: G92805XC GlyGen: G92805XC

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	7		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G91845HM GlyCosmos: G91845HM GlyGen: G91845HM

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J	7		N-Glycosylation	Interactions Focus chain J Interactions & Density Focus chain J
Glycosylation Resources
GlyTouCan: G46836GH GlyCosmos: G46836GH GlyGen: G46836GH

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K	4		N-Glycosylation	Interactions Focus chain K Interactions & Density Focus chain K
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	P	8		N-Glycosylation	Interactions Focus chain P Interactions & Density Focus chain P
Glycosylation Resources
GlyTouCan: G34499SX GlyCosmos: G34499SX GlyGen: G34499SX

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain X [auth B] SDF format, chain Q [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain R [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	Q [auth A], R [auth A], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain Q [auth A] Focus chain R [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
IFM Query on IFM Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain W [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain W [auth A]	EA [auth B], W [auth A]	5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE C₆ H₁₃ N O₃ QPYJXFZUIJOGNX-HSUXUTPPSA-N		Interactions Focus chain EA [auth B] Focus chain W [auth A] Interactions & Density Focus chain EA [auth B] Focus chain W [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain U [auth A] MOL2 format, chain U [auth A]	U [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain U [auth A] Interactions & Density Focus chain U [auth A]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain S [auth A] SDF format, chain T [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A]	AA [auth B], BA [auth B], CA [auth B], S [auth A], T [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain S [auth A] Focus chain T [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain V [auth A] SDF format, chain DA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain DA [auth B]	DA [auth B], V [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain V [auth A] Interactions & Density Focus chain DA [auth B] Focus chain V [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
IFM	Binding MOAD: 4IIC	Ki: 1.40e+4 (nM) from 1 assay(s)
IFM	PDBBind: 4IIC	Ki: 1.40e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.184
R-Value Work: 0.145
R-Value Observed: 0.147
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.142	α = 90
b = 122.478	β = 90
c = 222.107	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-04-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-04-10
Type: Initial release
Version 1.1: 2013-07-31
Changes: Database references
Version 1.2: 2015-08-12
Changes: Non-polymer description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary