SMTL ID : 2d7i.1

Crystal structure of pp-GalNAc-T10 with UDP, GalNAc and Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 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: 6 residues within 4Å: Chain A: R.53, N.91, H.133, N.137, L.169, F.170 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.137

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

NAG.2: 4 residues within 4Å: Chain A: P.423, N.560, T.562, V.563 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.423, A:V.563 Hydrogen bonds: A:N.560 NAG.4: 4 residues within 4Å: Chain A: N.113, A.145, T.196, D.198 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.145 Hydrogen bonds: A:N.113, A:T.196, A:T.196

1 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Non-covalent)

NGA.3: 11 residues within 4Å: Chain A: L.184, R.188, D.204, A.285, G.286, G.287, W.309, G.310, E.312, H.337 Ligands: UDP.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.188, A:R.188, A:D.204, A:G.286, A:G.287, A:G.310, A:E.312

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.5: 4 residues within 4Å: Chain A: D.204, H.206, H.337 Ligands: UDP.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:H.206, A:H.337, H2O.1

1 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.6: 18 residues within 4Å: Chain A: P.119, F.120, H.121, E.123, D.152, R.181, G.183, L.184, D.204, S.205, H.206, I.308, W.309, H.337, R.340, Y.345 Ligands: NGA.3, MN.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.345 Hydrogen bonds: A:H.121, A:E.123, A:D.152, A:R.181, A:L.184, A:S.205, A:S.205, A:S.205, A:R.340, A:Y.345 Salt bridges: A:H.206, A:H.337, A:R.340

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kubota, T. et al., Structural basis of carbohydrate transfer activity by human UDP-GalNAc: polypeptide alpha-N-acetylgalactosaminyltransferase (pp-GalNAc-T10). J.Mol.Biol. (2006)

Release Date

2006-11-07

Peptides

Polypeptide N-acetylgalactosaminyltransferase 10: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polypeptide N-acetylgalactosaminyltransferase 10

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