SMTL ID : 3cu0.1

human beta 1,3-glucuronyltransferase I (GlcAT-I) in complex with UDP and GAL-GAL(6-SO4)-XYL(2-PO4)-O-SER

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x GAL- GAL: beta-D-galactopyranose-(1-3)-beta-D-galactopyranose(Non-covalent)

GAL-GAL.1: 12 residues within 4Å: Chain A: V.167, G.168, G.169, E.173, W.189, R.193, V.197, D.198, R.223, G.224, E.227 Ligands: SO4.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:E.173, A:R.193, A:R.193, A:D.198, A:G.224 Water bridges: A:G.168, A:V.197, A:E.227, A:E.227, A:E.227, A:E.227 GAL-GAL.2: 12 residues within 4Å: Chain B: V.167, G.168, G.169, E.173, W.189, R.193, V.197, D.198, R.223, G.224, E.227 Ligands: SO4.7 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:E.173, B:R.193, B:R.193, B:D.198, B:D.198, B:G.224 Water bridges: B:G.168, B:G.168, B:V.197, B:E.227, B:E.227

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

MN.3: 2 residues within 4Å: Chain A: D.142 Ligands: UDP.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.142, A:D.142, H2O.1, H2O.1 MN.8: 3 residues within 4Å: Chain B: D.142, R.256 Ligands: UDP.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.142, B:D.142, H2O.6, H2O.6

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: G.169, W.189 Chain B: K.263, Q.264 Ligands: GAL-GAL.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.263, B:Q.264, B:Q.264 SO4.7: 5 residues within 4Å: Chain A: K.263, Q.264 Chain B: G.169, W.189 Ligands: GAL-GAL.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.263, A:Q.264, A:Q.264

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

UDP.5: 14 residues within 4Å: Chain A: P.28, T.29, Y.30, R.32, D.59, R.102, G.103, R.107, D.140, D.141, D.142, H.254, R.256 Ligands: MN.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:R.102 Hydrogen bonds: A:Y.30, A:R.32, A:R.32, A:D.59, A:D.59, A:D.141, A:D.141, A:R.256 Water bridges: A:T.85, A:R.102, A:R.102, A:G.103, A:D.140, A:D.140, A:D.140, A:H.254 Salt bridges: A:R.102, A:R.102, A:H.254, A:R.256 pi-Stacking: A:Y.30 UDP.6: 15 residues within 4Å: Chain B: P.28, T.29, Y.30, R.32, D.59, P.101, R.102, G.103, R.107, D.140, D.141, D.142, H.254, R.256 Ligands: MN.8 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:R.32, B:D.59, B:D.59, B:D.141, B:D.141 Water bridges: B:R.32, B:R.102, B:Q.106, B:R.256, B:R.256 Salt bridges: B:H.254, B:R.256, B:R.256 pi-Stacking: B:Y.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tone, Y. et al., 2-o-phosphorylation of xylose and 6-o-sulfation of galactose in the protein linkage region of glycosaminoglycans influence the glucuronyltransferase-I activity involved in the linkage region synthesis. J.Biol.Chem. (2008)

Release Date

2008-05-06

Peptides

Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3