SMTL ID : 1v84.1

Crystal structure of human GlcAT-P in complex with N-acetyllactosamine, Udp, and Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

1 x NDG- GAL: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG-GAL.1: 11 residues within 4Å: Chain A: G.142, E.147, F.164, R.168, I.172, D.173, G.199, G.200, E.203 Chain B: V.239, N.240 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.147, A:R.168, A:R.168, A:D.173, B:N.240, A:G.142, A:G.199 Water bridges: A:G.142, A:I.172, A:G.200, A:E.203, A:E.203, A:G.199 Hydrophobic interactions: B:V.239

1 x NAG- GAL: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-GAL.2: 12 residues within 4Å: Chain A: V.239, N.240 Chain B: G.142, G.143, E.147, F.164, R.168, I.172, D.173, G.199, G.200, E.203 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.147, B:R.168, B:R.168, B:D.173, B:G.142, B:G.199, A:N.240 Water bridges: B:G.142, B:I.172, B:D.173, B:G.200, B:G.200, B:E.203 Hydrophobic interactions: A:V.239

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

MN.3: 2 residues within 4Å: Chain A: D.116 Ligands: UDP.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.116, A:D.116, H2O.1, H2O.1 MN.6: 3 residues within 4Å: Chain B: D.116, R.232 Ligands: UDP.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.116, B:D.116, H2O.7, H2O.7

1 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.4: 5 residues within 4Å: Chain A: R.150, R.159, W.160, H.167 Chain B: F.246 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.150, A:W.160, A:W.160 Salt bridges: A:R.150, A:R.150, A:H.167

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

UDP.5: 15 residues within 4Å: Chain A: P.10, T.11, Y.12, R.14, D.41, K.72, R.84, G.85, R.89, D.114, D.115, D.116, H.230, R.232 Ligands: MN.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:R.84 Hydrogen bonds: A:Y.12, A:R.14, A:R.14, A:D.41, A:K.72, A:R.89, A:D.115, A:D.115 Water bridges: A:N.117 Salt bridges: A:R.84, A:R.84, A:H.230, A:R.232, A:R.232 pi-Stacking: A:Y.12 UDP.7: 14 residues within 4Å: Chain B: P.10, T.11, Y.12, R.14, D.41, R.84, G.85, R.89, D.114, D.115, D.116, H.230, R.232 Ligands: MN.6 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:Y.12, B:R.14, B:R.14, B:D.41, B:D.41, B:R.84, B:D.115, B:D.115 Water bridges: B:Q.88, B:D.114, B:D.114, B:D.114 Salt bridges: B:R.84, B:H.230, B:R.232, B:R.232 pi-Stacking: B:Y.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kakuda, S. et al., Structural Basis for Acceptor Substrate Recognition of a Human Glucuronyltransferase, GlcAT-P, an Enzyme Critical in the Biosynthesis of the Carbohydrate Epitope HNK-1. J.Biol.Chem. (2004)

Release Date

2004-05-25

Peptides

Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1

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