SMTL ID : 2wgz.1

Crystal structure of alpha-1,3 galactosyltransferase (alpha3GT) in a complex with p-nitrophenyl-beta-galactoside (pNP-beta-Gal)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-dimer

Ligands

1 x 147: 4-nitrophenyl beta-D-galactopyranoside(Non-covalent)

147.1: 10 residues within 4Å: Chain A: Q.168, W.170, W.171, T.180, Y.199, W.235, E.238, W.277, K.280 Ligands: UDP.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.168, A:T.180, A:E.238 Water bridges: A:H.201, A:K.280, A:Y.282 pi-Stacking: A:W.170, A:W.170

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

MN.2: 4 residues within 4Å: Chain A: D.146, D.148, K.280 Ligands: UDP.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.146, A:D.148, A:D.148, H2O.11 MN.10: 4 residues within 4Å: Chain B: D.146, D.148, K.280 Ligands: UDP.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.146, B:D.148, B:D.148, H2O.21

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

UDP.3: 16 residues within 4Å: Chain A: F.55, A.56, V.57, Y.60, W.116, I.119, S.120, R.123, D.146, V.147, D.148, K.280, Y.282, R.286 Ligands: 147.1, MN.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.119 Hydrogen bonds: A:F.55, A:V.57, A:V.57, A:Y.60, A:V.147, A:D.148, A:Y.282, A:Y.282 Water bridges: A:S.120, A:R.123, A:K.280, A:K.280, A:R.286, A:R.286 Salt bridges: A:K.280, A:K.280, A:R.286, A:R.286 pi-Stacking: A:Y.60 UDP.11: 16 residues within 4Å: Chain B: F.55, A.56, V.57, Y.60, W.116, I.119, S.120, R.123, D.146, V.147, D.148, K.280, Y.282, R.286 Ligands: GAL.8, MN.10 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.119 Hydrogen bonds: B:F.55, B:V.57, B:V.57, B:Y.60, B:Y.60, B:V.147, B:D.148, B:Y.282 Water bridges: B:R.123, B:K.280, B:K.280, B:Y.282, B:R.286, B:R.286 Salt bridges: B:K.280, B:K.280, B:R.286, B:R.286 pi-Stacking: B:Y.60

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: A.188, A.189, E.218, C.219, H.240, K.243, Y.244 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.188, A:E.218, A:H.240 Water bridges: A:N.248 GOL.5: 7 residues within 4Å: Chain A: K.47, T.49, H.137, E.138, V.139, D.140 Chain B: K.47 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.47, B:K.47, A:T.49, A:V.139 GOL.6: 7 residues within 4Å: Chain A: K.47 Chain B: T.49, Q.136, H.137, E.138, V.139, D.140 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.49, B:H.137, A:K.47, A:K.47 GOL.7: 4 residues within 4Å: Chain A: H.63, E.67, Q.278, E.281 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.63, A:Q.278, A:Q.278, A:E.281 GOL.12: 8 residues within 4Å: Chain B: A.188, A.189, E.218, G.222, H.240, K.243, Y.244, L.247 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.188, B:H.240 Water bridges: B:G.222, B:N.248, B:N.248 GOL.13: 4 residues within 4Å: Chain B: H.63, E.67, Q.278, E.281 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.63, B:E.67, B:Q.278

1 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.8: 11 residues within 4Å: Chain B: Q.168, W.171, T.180, Y.199, H.201, W.235, E.238, W.277, K.280 Ligands: NPO.9, UDP.11 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.168, B:T.180, B:T.180, B:E.238, B:K.280 Water bridges: B:H.201, B:K.280

1 x NPO: P-NITROPHENOL(Non-covalent)

NPO.9: 4 residues within 4Å: Chain B: Q.168, W.170, W.277 Ligands: GAL.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.168 pi-Stacking: B:W.170, B:W.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jamaluddin, H. et al., Crystal Structure of Alpha-1,3 Galactosyltransferase (Alpha3Gt) in a Complex with P-Nitrophenyl-Beta-Galactoside (Pnpbetagal). Biochem.Biophys.Res.Commun. (2009)

Release Date

2009-06-16

Peptides

N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYL TRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYL TRANSFERASE