SMTL ID : 5bo9.1

Structure of human sialyltransferase ST8SiaIII in complex with CMP-3FNeu5Ac and Sia-6S-LacNAc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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.1: 2 residues within 4Å: Chain A: N.36, A.39 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: Y.102, D.127, R.146, K.147, T.148, N.149 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.146 NAG-NAG.5: 7 residues within 4Å: Chain B: H.50, V.51, D.52, K.55, N.56, H.227, R.230 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain B: Y.102, D.127, 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.2: 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 NGS- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose

NGS-GAL-SIA.4: 15 residues within 4Å: Chain A: Y.74, N.154, P.155, S.156, P.189, F.192, F.193, T.195, S.196, R.241, T.244, E.295, S.296, H.297 Ligands: CSF.9 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.195, A:R.241, A:R.241, A:S.296, A:N.154, A:N.154, A:S.156, A:S.156, A:P.189, A:R.241 Salt bridges: A:R.241 Hydrophobic interactions: A:Y.74, A:F.192 Water bridges: A:S.196 NGS-GAL-SIA.7: 12 residues within 4Å: Chain B: Y.74, N.154, P.155, S.156, P.189, F.192, F.193, T.195, S.196, R.241, T.244 Ligands: CSF.12 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:T.195, B:R.241, B:R.241, B:N.154, B:N.154, B:S.156, B:S.156, B:P.189, B:R.241, B:T.244 Salt bridges: B:R.241 Hydrophobic interactions: B:Y.74, B:F.192 Water bridges: B:F.192

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

NAG.8: 7 residues within 4Å: Chain A: H.50, V.51, D.52, K.55, N.56, I.224, H.227 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.55 Hydrogen bonds: A:D.52, A:K.55 Water bridges: A:G.222 NAG.10: 2 residues within 4Å: Chain B: N.36, A.39 No protein-ligand interaction detected (PLIP) NAG.11: 2 residues within 4Å: Chain B: N.103, I.104 No protein-ligand interaction detected (PLIP)

2 x CSF: CYTIDINE-5'-MONOPHOSPHATE-3-FLUORO-N-ACETYL-NEURAMINIC ACID(Non-covalent)

CSF.9: 20 residues within 4Å: Chain A: G.109, N.110, S.111, C.132, N.133, N.154, I.157, Y.161, S.243, T.244, G.245, G.263, F.264, W.265, P.266, Y.279, H.280, Y.282, H.297 Ligands: NGS-GAL-SIA.4 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.110, A:N.110, A:N.133, A:N.154, A:S.243, A:S.243, A:S.243, A:T.244, A:G.245, A:W.265, A:Y.279, A:Y.279, A:H.280, A:Y.282 Water bridges: A:G.112, A:E.302 Salt bridges: A:H.280, A:H.297 CSF.12: 19 residues within 4Å: Chain B: G.109, N.110, S.111, C.132, N.133, N.154, S.156, I.157, Y.161, S.243, T.244, G.245, G.263, F.264, W.265, P.266, Y.279, H.280 Ligands: NGS-GAL-SIA.7 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.279 Hydrogen bonds: B:N.110, B:N.110, B:N.133, B:N.154, B:S.156, B:S.243, B:S.243, B:S.243, B:T.244, B:T.244, B:G.245, B:W.265, B:W.265, B:H.280 Salt bridges: B:H.280

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Volkers, G. et al., Structure of human ST8SiaIII sialyltransferase provides insight into cell-surface polysialylation. Nat.Struct.Mol.Biol. (2015)

Release Date

2015-07-15

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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