SMTL ID : 6e4q.1 (3 other biounits)

Crystal Structure of the Drosophila Melanogaster Polypeptide N-Acetylgalactosaminyl Transferase PGANT9A in Complex with UDP and Mn2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: D.161, H.163, H.297 Ligands: UDP.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.161, A:H.163, A:H.297, H2O.1

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

NAG.2: 3 residues within 4Å: Chain A: N.181, T.183, G.284 No protein-ligand interaction detected (PLIP)

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

UDP.3: 14 residues within 4Å: Chain A: C.76, F.77, H.78, D.109, R.138, G.140, L.141, D.161, S.162, H.163, H.297, R.300, Y.305 Ligands: MN.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:H.78, A:Y.305 Hydrogen bonds: A:H.78, A:D.109, A:D.109, A:R.138, A:S.162, A:S.162, A:S.162, A:Y.305 Salt bridges: A:H.163, A:H.297, A:R.300

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

EDO.4: 2 residues within 4Å: Chain A: Y.123, Y.127 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.127 EDO.5: 3 residues within 4Å: Chain A: Y.461, T.501, L.502 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.461, A:Y.461, A:T.501, A:L.502

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ji, S. et al., A molecular switch orchestrates enzyme specificity and secretory granule morphology. Nat Commun (2018)

Release Date

2018-09-12

Peptides

polypeptide N-acetylgalactosaminyltransferase 9: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

polypeptide N-acetylgalactosaminyltransferase 9

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