SMTL ID : 5cxy.1

Structure of a Glycosyltransferase in Complex with Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 7 residues within 4Å: Chain A: H.50, V.51, D.52, K.55, N.56, H.227, R.230 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.55, A:K.55

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 2 residues within 4Å: Chain A: N.36, A.39 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: Y.102, D.127, R.146, K.147, T.148, N.149 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 8 residues within 4Å: Chain B: H.50, V.51, D.52, K.55, N.56, I.224, H.227, R.230 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.227, B:R.230 NAG-NAG.6: 6 residues within 4Å: Chain B: Y.102, D.127, R.146, K.147, T.148, N.149 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.3: 4 residues within 4Å: Chain A: N.103, I.104, E.258, H.260 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.104

2 x 55T: 5'-O-[(R)-[(S)-[3-(acetylamino)phenyl](phosphono)methoxy](hydroxy)phosphoryl]cytidine(Non-covalent)

55T.7: 19 residues within 4Å: Chain A: G.109, N.110, S.111, C.132, N.133, R.241, S.243, T.244, G.245, G.263, F.264, W.265, P.266, Y.279, H.280, W.293, Q.294, H.297, L.299 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Q.294 Hydrogen bonds: A:N.110, A:N.110, A:N.133, A:R.241, A:S.243, A:S.243, A:T.244, A:T.244, A:T.244, A:G.245, A:W.265, A:W.265, A:W.293, A:H.297, A:E.302 Water bridges: A:G.112, A:Y.282, A:Y.282 Salt bridges: A:H.280 pi-Stacking: A:H.297 55T.10: 18 residues within 4Å: Chain B: G.109, N.110, S.111, C.132, N.133, S.243, T.244, G.245, G.263, F.264, W.265, P.266, Y.279, H.280, W.293, S.296, H.297, L.299 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:W.293, B:W.293, B:L.299 Hydrogen bonds: B:N.110, B:N.110, B:N.133, B:S.243, B:S.243, B:T.244, B:T.244, B:G.245, B:W.265, B:Y.279, B:W.293, B:S.296, B:H.297, B:E.302 Water bridges: B:G.112, B:E.302 Salt bridges: B:H.280 pi-Stacking: B:H.297

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.8: 2 residues within 4Å: Chain B: N.36, A.39 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain B: N.103, I.104 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Volkers, G. et al., To be published. To be published

Release Date

2016-09-07

Peptides

Sia-alpha-2,3-Gal-beta-1,4-GlcNAc-R:alpha 2,8-sialyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Sia-alpha-2,3-Gal-beta-1,4-GlcNAc-R:alpha 2,8-sialyltransferase

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