SMTL ID : 2am5.1

Crystal Structure of N-Acetylglucosaminyltransferase I in Complex with UDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: D.108 Ligands: UDP.2, GOL.7 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.108, H2O.2, H2O.3, H2O.4

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

UDP.2: 18 residues within 4Å: Chain A: I.8, A.9, C.10, R.12, D.39, C.40, K.81, I.82, H.85, E.106, D.107, D.108, G.215, V.216, S.217 Ligands: MN.1, GOL.5, GOL.7 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.216 Hydrogen bonds: A:A.9, A:D.39, A:D.39, A:H.85, A:D.107, A:D.107, A:D.107, A:V.216, A:S.217, A:S.217 Water bridges: A:R.12, A:R.12, A:R.12, A:R.12, A:E.106 Salt bridges: A:R.12

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: R.26, A.29, P.33, I.34, S.54, A.55, V.56, T.57 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.26, A:R.26, A:I.34, A:I.34, A:T.57, A:T.57 GOL.4: 8 residues within 4Å: Chain A: Y.285, G.307, G.315, W.334, G.336, Y.337, D.338, W.341 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.285, A:D.338, A:D.338 GOL.5: 3 residues within 4Å: Chain A: D.11, V.216 Ligands: UDP.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.11 Water bridges: A:R.12, A:V.216 GOL.6: 6 residues within 4Å: Chain A: P.130, L.132, W.133, L.169, L.172, R.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.130, A:R.198 Water bridges: A:W.133 GOL.7: 6 residues within 4Å: Chain A: Y.79, I.82, E.106, D.186 Ligands: MN.1, UDP.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.106 Water bridges: A:E.106, A:D.186, A:D.186, A:D.186, A:D.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gordon, R.D. et al., X-ray Crystal Structures of Rabbit N-acetylglucosaminyltransferase I (GnT I) in Complex with Donor Substrate Analogues. J.Mol.Biol. (2006)

Release Date

2006-06-27

Peptides

Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase

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