SMTL ID : 5wd7.1

Structure of a bacterial polysialyltransferase in complex with fondaparinux

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

1 x ZDO- IDS- SUS- BDP- SGN: 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside(Non-covalent)

ZDO-IDS-SUS-BDP-SGN.1: 12 residues within 4Å: Chain A: Q.22, M.23, G.24, N.51, M.54, K.56, N.57, R.61, R.240, H.272, K.274, D.359 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.274, A:Q.22, A:R.240, A:K.56, A:K.56, A:N.57, A:N.57, A:N.51, A:N.57, A:R.61, A:K.274 Salt bridges: A:R.61, A:R.240, A:K.274, A:K.56, A:R.61, A:H.272, A:R.240

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain B: Y.352, K.353, E.354 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.354, B:E.355 SO4.3: 2 residues within 4Å: Chain B: K.95, K.99 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.95, B:K.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lizak, C. et al., X-ray crystallographic structure of a bacterial polysialyltransferase provides insight into the biosynthesis of capsular polysialic acid. Sci Rep (2017)

Release Date

2017-08-02

Peptides

SiaD: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
M

SiaD

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