5VMA

Structure of B. pumilus GH48 in complex with a cellobio-derived isofagomine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Bacillus pumilus family 48 glycoside hydrolase in complex with cellobio-derived isofagomine

Alahuhta, P.M.Lunin, V.V.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycoside hydrolase
A
709Bacillus pumilus (strain SAFR-032)Mutation(s): 0 
Find proteins for A8FDC4 (Bacillus pumilus (strain SAFR-032))
Go to UniProtKB:  A8FDC4
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MLI
Query on MLI

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A
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
9MR
Query on 9MR

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A
(3R,4R,5R)-3-HYDROXY-5-(HYDROXYMETHYL)PIPERIDIN-4-YL BETA-D-GLUCOPYRANOSIDE
CELLOBIOSE-LIKE ISOFAGOMINE
C12 H23 N O8
LEOSSOWHBSKZSO-WUYFHPBOSA-N
 Ligand Interaction
G2I
Query on G2I

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A
(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl 4-O-beta-D-glucopyranosyl-beta-D-glucopyranoside
Cellotriose-like isofagomine, Cellobiosyl isofagomine
C18 H33 N O13
ZIMIYDWQNDRGNF-IONZOCAKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.154 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 98.891α = 90.00
b = 98.891β = 90.00
c = 216.799γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata processing
MOLREPphasing
PROTEUM PLUSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United States--

Revision History 

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2019-12-04
    Type: Author supporting evidence