7EY1

Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose

Gong, W.M.Yang, L.Y.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-D-xylosidase/beta-D-glucosidaseA, B, C, D803Lentinula edodesMutation(s): 0 
Gene Names: Lxyl-p1-2
UniProt
Find proteins for G8GLP2 (Lentinula edodes)
Explore G8GLP2 
Go to UniProtKB:  G8GLP2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG8GLP2
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-glucopyranoseE, G 8N/AN/A Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(4-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF 4N/AN-Glycosylation Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth I],
J [auth K],
L [auth M]
3N/AN-Glycosylation Oligosaccharides Interaction
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth J]4N/AN/A Oligosaccharides Interaction
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(6-4)]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-glucopyranoseK [auth L]8N/AN/A Oligosaccharides Interaction
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-beta-D-mannopyranoseM [auth N]2N/AN/A Oligosaccharides Interaction
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BKR (Subject of Investigation/LOI)
Query on BKR

Download Ideal Coordinates CCD File 
DA [auth B],
U [auth A]
Deacetyltaxol
C45 H49 N O13
TYLVGQKNNUHXIP-MHHARFCSSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth B],
BA [auth B],
CA [auth B],
GA [auth C],
HA [auth C],
AA [auth B],
BA [auth B],
CA [auth B],
GA [auth C],
HA [auth C],
IA [auth C],
KA [auth C],
LA [auth C],
MA [auth C],
N [auth A],
NA [auth D],
O [auth A],
OA [auth D],
P [auth A],
PA [auth D],
Q [auth A],
QA [auth D],
R [auth A],
RA [auth D],
S [auth A],
T [auth A],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

Download Ideal Coordinates CCD File 
JA [auth C]beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN
Query on MAN

Download Ideal Coordinates CCD File 
FA [auth B]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
XYZ (Subject of Investigation/LOI)
Query on XYZ

Download Ideal Coordinates CCD File 
EA [auth B]beta-D-xylofuranose
C5 H10 O5
HMFHBZSHGGEWLO-KKQCNMDGSA-N
 Ligand Interaction
XYP (Subject of Investigation/LOI)
Query on XYP

Download Ideal Coordinates CCD File 
V [auth A]beta-D-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 228.508α = 90
b = 88.174β = 90
c = 218.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31270796

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-01
    Type: Initial release
  • Version 2.0: 2022-06-15
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary