SMTL ID : 5bo6.1

Structure of human sialyltransferase ST8SiaIII in complex with CDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 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: 6 residues within 4Å: Chain A: H.50, V.51, D.52, K.55, N.56, H.227 No protein-ligand interaction detected (PLIP)

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: 3 residues within 4Å: Chain A: K.34, 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 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.147 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, K.125, H.260 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.104 Hydrogen bonds: A:K.125, A:K.125

2 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.7: 16 residues within 4Å: Chain A: 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, K.292, W.293 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.279 Hydrogen bonds: A:N.110, A:N.110, A:N.133, A:S.243, A:S.243, A:T.244, A:T.244, A:G.245, A:W.265, A:W.265, A:W.293 Water bridges: A:G.112, A:T.244, A:Y.282, A:Y.282, A:W.293 Salt bridges: A:H.280, A:K.292, A:K.292 CDP.10: 14 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 12 PLIP interactions: 12 interactions with chain B 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 Water bridges: B:G.112 Salt bridges: B:H.280

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 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.36 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., 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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