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 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycoside hydrolaseA709Bacillus pumilusMutation(s): 0 
Gene Names: BPUM_1559
UniProt
Find proteins for A8FDC4 (Bacillus pumilus (strain SAFR-032))
Explore A8FDC4 
Go to UniProtKB:  A8FDC4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8FDC4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G2I
Query on G2I

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl 4-O-beta-D-glucopyranosyl-beta-D-glucopyranoside
C18 H33 N O13
ZIMIYDWQNDRGNF-IONZOCAKSA-N
 Ligand Interaction
9MR
Query on 9MR

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D [auth A](3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl beta-D-glucopyranoside
C12 H23 N O8
LEOSSOWHBSKZSO-WUYFHPBOSA-N
 Ligand Interaction
MLI
Query on MLI

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T [auth A]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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U [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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E [auth A],
F [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-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 
  • R-Value Observed: 0.156 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.891α = 90
b = 98.891β = 90
c = 216.799γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata collection
PROTEUM PLUSdata processing
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Derived calculations, Structure summary