SMTL ID : 2yk4.1

Structure of Neisseria LOS-specific sialyltransferase (NST).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

2 x EGC: 2-(2-{2-[2-(2-{2-[2-(2-{2-[4-(1,1,3,3-TETRAMETHYL-BUTYL)-PHENOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOX Y}-ETHOXY)-ETHANOL(Non-covalent)

EGC.1: 22 residues within 4Å: Chain A: Y.9, M.34, Y.63, G.64, L.65, N.66, S.68, I.101, A.103, F.104, T.107 Chain B: F.7, V.32, W.55, F.59, L.96, E.97, V.99, S.100, I.101, D.151 Ligands: EGC.6 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:V.32, B:W.55, B:W.55, A:L.65, A:L.65, A:F.104 Hydrogen bonds: B:S.100, A:S.68, A:S.100, A:A.103, A:F.104 pi-Stacking: B:F.7, A:F.104 EGC.6: 22 residues within 4Å: Chain A: F.7, V.32, W.55, F.59, L.96, E.97, V.99, S.100, I.101, D.151 Chain B: Y.9, M.34, Y.63, G.64, L.65, N.66, S.68, I.101, A.103, F.104, T.107 Ligands: EGC.1 13 PLIP interactions: 5 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:V.32, A:W.55, A:W.55, B:L.65, B:L.65, B:F.104 Hydrogen bonds: A:S.100, B:S.68, B:S.100, B:A.103, B:F.104 pi-Stacking: A:F.7, B:F.104

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: D.117, D.118, G.119, I.167 Chain B: L.12, Q.13, V.16 No protein-ligand interaction detected (PLIP) EDO.3: 4 residues within 4Å: Chain A: H.233, S.275, G.276 Chain B: F.71 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.275, A:G.276 Water bridges: A:T.120, B:N.70 EDO.4: 2 residues within 4Å: Chain A: A.22, Q.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.22 Water bridges: A:R.19 EDO.7: 7 residues within 4Å: Chain A: L.12, Q.13, V.16 Chain B: D.117, D.118, G.119, I.167 No protein-ligand interaction detected (PLIP) EDO.8: 4 residues within 4Å: Chain A: F.71 Chain B: H.233, S.275, G.276 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.275, B:G.276 Water bridges: B:T.120, A:N.70 EDO.9: 2 residues within 4Å: Chain B: A.22, Q.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.22 Water bridges: B:R.19

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

SO4.5: 3 residues within 4Å: Chain A: H.24, E.27 Chain B: R.90 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:R.90 Salt bridges: B:K.89, B:R.90, A:H.24 SO4.10: 3 residues within 4Å: Chain A: R.90 Chain B: H.24, E.27 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:H.24, A:K.89, A:R.90 Water bridges: A:R.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, L.Y.C. et al., Structure and Mechanism of the Lipooligosaccharide Sialyltransferase from Neisseria Meningitidis. J.Biol.Chem. (2011)

Release Date

2011-08-31

Peptides

CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE