ISDA

Deposition Date 2015-06-09

Release Date 2015-09-09

Last Version Date 2024-11-13

Entry Detail

PDB ID:

5BXR

Keywords:

HYDROLASE

Title:

LNBase in complex with LNB-NHAcDNJ

Biological Source:

Source Organism:

Bifidobacterium bifidum JCM 1254 (Taxon ID: 398514)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.60 Å

R-Value Free:

0.21

R-Value Work:

0.18

R-Value Observed:

0.18

Space Group:

P 21 21 2

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Lacto-N-biosidase
Gene (Uniprot):lnbB
Chain IDs:A, B
Chain Length:644
Number of Molecules:2
Biological Source:Bifidobacterium bifidum JCM 1254

UniProt ID:B3TLD6 Pfam ID:PF02838, PF00728, PF14200 EC:3.2.1.140

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
GAL	C	GAL	-D

Ligand Molecules

GAL

NOK

SO4

Primary Citation

Gaining insight into the catalysis by GH20 lacto-N-biosidase using small molecule inhibitors and structural analysis

Hattie, M, Ito, T, Debowski, A.W, Arakawa, T, Katayama, T, Yamamoto, K, Fushinobu, S, Stubbs, K.A, Ito, T, Katayama, T, Hattie, M, Sakurama, H, Wada, J, Suzuki, R, Ashida, H, Wakagi, T, Yamamoto, K, Stubbs, K.A, Fushinobu, S.Show

Chem.Commun.(Camb.) 51 15008 15011 (2015)

PMID: 26312778 DOI: 10.1039/c5cc05494j

Abstact

The synthesis of potent inhibitors for lacto-N-biosidases and X-ray structural characterization of these compounds in complex with BbLNBase is described.

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Protein

Chemical

Disease

Primary Citation of related structures