4ZFM

Structure of Gan1D-E170Q in complex with cellobiose-6-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structure of Gan1D-E170Q in complex with cellobiose-6-phosphate

Lansky, S.Zehavi, A.Dvir, H.Shoham, Y.Shoham, G.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 6-phospho-beta-galactobiosidase
A, B, C, D
485Geobacillus stearothermophilusMutation(s): 1 
Gene Names: gan1D
EC: 3.2.1.85
UniProt
Find proteins for W8QF82 (Geobacillus stearothermophilus)
Explore W8QF82 
Go to UniProtKB:  W8QF82
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW8QF82
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
1,5-anhydro-6-O-phosphono-D-glucitol-(1-4)-beta-D-glucopyranose
E
2N/A
Glycosylation Resources
GlyTouCan:  G15380AW
GlyCosmos:  G15380AW
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BG6
Query on BG6

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F [auth A],
M [auth B]
6-O-phosphono-beta-D-glucopyranose
C6 H13 O9 P
NBSCHQHZLSJFNQ-VFUOTHLCSA-N
0WK
Query on 0WK

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U [auth C]1,5-anhydro-6-O-phosphono-D-glucitol
C6 H13 O8 P
KAJAXXUCVJFKFM-SLPGGIOYSA-N
BGC
Query on BGC

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V [auth C]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
GOL
Query on GOL

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G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
N [auth B],
O [auth B],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
W [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD
Query on IMD

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L [auth A],
T [auth C],
X [auth D]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.59α = 90
b = 97.47β = 97.66
c = 105.27γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary