RCSB Protein Data Bank - RCSB PDB - 2V3D Structure Summary

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ACID-BETA-GLUCOSIDASE WITH N-BUTYL-DEOXYNOJIRIMYCIN

DOI:10.2210/pdb2v3d/pdb

2V3D

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Primary Citation

Related Citations in PDB Entry (REMARK 1) Hide

Molecular Description

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Source

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Polymer: 1

Scientific Name:

Homo sapiens

Taxonomy

Common Name:

Human

Expression System:

Daucus carota

Polymer: 2

Scientific Name:

Synthetic construct

Taxonomy

Related PDB Entries

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Identifier	Details
1OGS	HUMAN ACID-BETA-GLUCOSIDASE
1Y7V	X-RAY STRUCTURE OF HUMAN ACID-BETA- GLUCOSIDASE COVALENTLYBOUND TO CONDURITOL B EPOXIDE
2F61	CRYSTAL STRUCTURE OF PARTIALLY DEGLYCOSYLATED ACID BETA-GLUCOSIDASE
2J25	PARTIALLY DEGLYCOSYLATED GLUCOCERAMIDASE
2V3E	ACID-BETA-GLUCOSIDASE WITH N-NONYL- DEOXYNOJIRIMYCIN
2V3F	ACID-BETA-GLUCOSIDASE PRODUCED IN CARROT

Ligand Chemical Component

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Identifier	Formula	Name	Interactions
BMA Search Download	C₆ H₁₂ O₆	BETA-D-MANNOSE		Ligand Explorer
FUC Search Download	C₆ H₁₂ O₅	ALPHA-L-FUCOSE		Ligand Explorer
NAG Search Download	C₈ H₁₅ N O₆	N-ACETYL-D-GLUCOSAMINE		Ligand Explorer
NBV Search Download	C₁₀ H₂₁ N O₄	(2R,3R,4R,5S)-1-BUTYL-2-(HYDROXYMETHYL)PIPERIDINE- 3,4,5-TRIOL		Ligand Explorer
SO4 Search Download	O₄ S	SULFATE ION		Ligand Explorer

External Ligand Annotations

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Identifier

Binding Affinity (Sequence Identity %)

IC50:	270000 - 400000 nM (99)	- data from BindingDB
Ki:	116000 nM (99)	- data from BindingDB
Ki:	116000 nM	- data from BindingMOAD
Ki:	116000 nM	- data from PDBbind

External Domain Annotations Hide
SCOP Classification v1.75: 4 Domains - data from SCOP

CATH Classification v3.4.0: 4 Domains - data from CATH

Pfam Classification: 1 Domain - data from Pfam

GO Terms: 24 Terms - data from GO
Structural Biology Knowledgebase Data Hide

Data in orange boxes are gathered from external resources (when available).

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Biological Assembly 1

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Biological assembly 1 assigned by authors and generated by PQS (software)

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Deposition Summary

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Authors: Brumshtein, B., Greenblatt, H.M., Butters, T.D., Shaaltiel, Y., Aviezer, D., Silman, I., Futerman, A.H., Sussman, J.L.

Deposition:	2007-06-17
Release:	2007-08-14
Last Modified (REVDAT):	2009-02-24

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2011-07-13
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Experimental Details

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Method: X-RAY DIFFRACTION
Exp. Data:
Structure Factors
EDS

Unit Cell:
	Length [Å]	Angles [°]
	a = 67.99	α = 90.00
	b = 97.21	β = 102.91
	c = 82.41	γ = 90.00