SMTL ID : 4irp.1 (2 other biounits)

Crystal structure of catalytic domain of human beta1,4-galactosyltransferase-7 in open conformation with manganses and UDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

UDP.1: 11 residues within 4Å: Chain A: P.24, F.25, R.26, R.28, F.63, R.65, D.87, V.88, D.89, Y.118 Ligands: MN.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.63 Hydrogen bonds: A:P.24, A:R.26, A:R.26, A:R.28, A:D.87, A:V.88, A:D.89, A:D.89 Water bridges: A:Y.123, A:Y.123 Salt bridges: A:R.28 pi-Cation interactions: A:R.28

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

MN.2: 3 residues within 4Å: Chain A: D.89, H.181 Ligands: UDP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.89, A:D.89, A:H.181, H2O.6

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 4 residues within 4Å: Chain A: R.62, F.63, W.146, G.147 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.63 Hydrogen bonds: A:F.63 Salt bridges: A:R.62 ACT.4: 3 residues within 4Å: Chain A: D.3, P.5, R.41 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.41 ACT.5: 2 residues within 4Å: Chain A: G.15, P.16 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.16 ACT.6: 3 residues within 4Å: Chain A: D.98, G.100, F.101 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.101

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.7: 2 residues within 4Å: Chain A: A.104, F.167 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.105 pi-Stacking: A:F.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsutsui, Y. et al., Crystal Structures of beta-1,4-Galactosyltransferase 7 Enzyme Reveal Conformational Changes and Substrate Binding. J.Biol.Chem. (2013)

Release Date

2013-09-25

Peptides

Beta-1,4-galactosyltransferase 7: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-1,4-galactosyltransferase 7

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