2WCG | pdb_00002wcg

X-ray structure of acid-beta-glucosidase with N-octyl(cyclic guanidine)-nojirimycin in the active site

PDB DOI: https://doi.org/10.2210/pdb2WCG/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Daucus carota
Mutation(s): No

Deposited: 2009-03-12 Released: 2009-11-24
Deposition Author(s): Brumshtein, B., Aguilar, M., Garcia-Moreno, M.I., Mellet, C.O., Garcia-Fernandez, J.M., Silman, I., Shaaltiel, Y., Aviezer, D., Sussman, J.L., Futerman, A.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.194 (Depositor), 0.196 (DCC)
R-Value Work:
0.135 (Depositor), 0.136 (DCC)
R-Value Observed:
0.138 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.2 of the entry. See complete history.

Literature

6-Amino-6-Deoxy-5,6-Di-N-(N'-Octyliminomethylidene)Nojirimycin: Synthesis, Biological Evaluation, and Crystal Structure in Complex with Acid Beta-Glucosidase.

Brumshtein, B., Aguilar-Moncayo, M., Garcia-Moreno, M.I., Ortiz Mellet, C., Garcia Fernandez, J.M., Silman, I., Shaaltiel, Y., Aviezer, D., Sussman, J.L., Futerman, A.H.

(2009) Chembiochem 10: 1480

PubMed: 19437524 Search on PubMed
DOI: https://doi.org/10.1002/cbic.200900142
Primary Citation Related Structures:
2WCG

Organizational Affiliation

Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.

Macromolecule Content

Total Structure Weight: 116.54 kDa
Atom Count: 8,672
Modeled Residue Count: 988
Deposited Residue Count: 1,010
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUCOSYLCERAMIDASE	A, B	505	Homo sapiens	Mutation(s): 0 EC: 3.2.1.45 (PDB Primary Data), 3.2.1.46 (UniProt), 2.4.1 (UniProt), 3.2.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P04062 (Homo sapiens) Explore P04062 Go to UniProtKB: P04062
PHAROS: P04062 GTEx: ENSG00000177628
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04062
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: P04062-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MT5 Query on MT5 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain U [auth B] MOL2 format, chain L [auth A] MOL2 format, chain U [auth B] mmCIF format, chain L [auth A] mmCIF format, chain U [auth B]	L [auth A], U [auth B]	N-[(3E,5R,6R,7S,8R,8AR)-5,6,7,8-TETRAHYDROXYHEXAHYDROIMIDAZO[1,5-A]PYRIDIN-3(2H)-YLIDENE]OCTAN-1-AMINIUM C₁₅ H₃₀ N₃ O₄ DGGJYTDCPYQDLL-RKQHYHRCSA-O		Interactions Focus chain L [auth A] Focus chain U [auth B] Interactions & Density Focus chain L [auth A] Focus chain U [auth B]
FUC Query on FUC Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] mmCIF format, chain E [auth A] mmCIF format, chain N [auth B]	E [auth A], N [auth B]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain E [auth A] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain N [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain V [auth B] MOL2 format, chain M [auth A] MOL2 format, chain V [auth B] mmCIF format, chain M [auth A] mmCIF format, chain V [auth B]	M [auth A], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth A] Focus chain V [auth B] Interactions & Density Focus chain M [auth A] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.194 (Depositor), 0.196 (DCC)
R-Value Work: 0.135 (Depositor), 0.136 (DCC)
R-Value Observed: 0.138 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.311	α = 90
b = 96.827	β = 104.34
c = 83.234	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-11-24

Deposition Author(s):

Garcia-Fernandez, J.M.

Revision History (Full details and data files)

Version 1.0: 2009-11-24
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2017-11-15
Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Structure summary
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 3.1: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary
Version 3.2: 2024-10-16
Changes: Structure summary

2WCG | pdb_00002wcg

X-ray structure of acid-beta-glucosidase with N-octyl(cyclic guanidine)-nojirimycin in the active site

Literature

6-Amino-6-Deoxy-5,6-Di-N-(N'-Octyliminomethylidene)Nojirimycin: Synthesis, Biological Evaluation, and Crystal Structure in Complex with Acid Beta-Glucosidase.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

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