SMTL ID : 6wmo.1

Human poly-N-acetyl-lactosamine synthase structure demonstrates a modular assembly of catalytic subsites for GT-A glycosyltransferases

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x GAL- NAG- GAL: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose

GAL-NAG-GAL.1: 9 residues within 4Å: Chain A: I.243, H.244, A.246, H.249, Y.256, Y.270, I.298, D.300, F.323 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.300, A:Y.270 Water bridges: A:H.249, A:Y.267, A:Y.270, A:Y.270 Hydrophobic interactions: A:I.243, A:A.246 GAL-NAG-GAL.3: 13 residues within 4Å: Chain B: I.243, H.244, N.245, A.246, H.249, Y.256, Y.267, Y.270, I.298, D.300, V.301, F.323 Ligands: GOL.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.270, B:D.300, B:Y.270 Water bridges: B:Y.256, B:Y.267, B:Y.267, B:H.249 Hydrophobic interactions: B:A.246

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 12 residues within 4Å: Chain A: C.63, P.65, R.82, D.85, F.86, Y.89, Y.95, Y.180, R.181, T.183, F.185, N.186 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.95 Hydrogen bonds: A:D.85, A:Y.89 Water bridges: A:R.181 NAG-NAG-BMA-MAN.4: 11 residues within 4Å: Chain B: C.63, R.82, D.85, F.86, Y.89, Y.95, Y.180, R.181, T.183, F.185, N.186 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.89 Hydrogen bonds: B:D.85, B:Y.95

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: D.214, H.343 Ligands: UDP.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.214, A:H.343, H2O.1, H2O.3 MG.10: 4 residues within 4Å: Chain B: D.214, H.343 Ligands: UDP.11, EDO.14 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.343, H2O.5

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

UDP.6: 16 residues within 4Å: Chain A: K.116, S.117, L.118, H.121, D.182, T.183, F.184, L.187, K.190, D.212, D.213, D.214, K.255, Y.256, H.343 Ligands: MG.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.118 Hydrogen bonds: A:H.121, A:D.182, A:D.213, A:D.213, A:Y.256 Water bridges: A:F.184, A:D.212, A:D.212, A:K.255 Salt bridges: A:K.255, A:K.255, A:H.343 UDP.11: 18 residues within 4Å: Chain B: K.116, S.117, L.118, H.121, D.182, T.183, F.184, L.187, K.190, D.212, D.213, K.255, Y.256, H.343 Ligands: MG.10, EDO.14, GOL.15, EDO.16 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.118 Hydrogen bonds: B:H.121, B:D.182, B:D.182, B:D.213, B:D.213 Water bridges: B:T.183, B:D.214 Salt bridges: B:K.255, B:K.255, B:H.343

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.7: 4 residues within 4Å: Chain A: N.61, C.63, N.94, Y.95 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.95 Hydrogen bonds: A:N.61, A:N.94 NAG.8: 3 residues within 4Å: Chain A: K.107, K.108, N.140 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.107, A:K.108, A:N.140 Water bridges: A:T.142 NAG.12: 4 residues within 4Å: Chain B: N.61, C.63, N.94, Y.95 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.95 Hydrogen bonds: B:N.61, B:N.94

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 4 residues within 4Å: Chain A: H.121, F.122, A.123, R.124 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.121, A:A.123, A:R.124, A:R.124 Water bridges: A:H.121, A:F.122 EDO.13: 4 residues within 4Å: Chain B: H.121, F.122, A.123, R.124 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.120, B:A.123, B:R.124, B:R.124, B:R.124 Water bridges: B:F.122 EDO.14: 5 residues within 4Å: Chain B: D.214, H.343, S.344 Ligands: MG.10, UDP.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.344 EDO.16: 8 residues within 4Å: Chain B: Y.256, G.272, G.273, G.274, T.322, H.343 Ligands: UDP.11, GOL.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.256, B:G.274 EDO.17: 3 residues within 4Å: Chain B: K.104, E.135, Q.173 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.104, B:E.135

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 11 residues within 4Å: Chain B: K.116, F.184, D.212, Y.256, G.273, G.274, D.299, D.300 Ligands: GAL-NAG-GAL.3, UDP.11, EDO.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.116, B:K.116, B:D.212, B:G.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kadirvelraj, R. et al., Comparison of human poly-N-acetyl-lactosamine synthase structure with GT-A fold glycosyltransferases supports a modular assembly of catalytic subsites. J.Biol.Chem. (2020)

Release Date

2020-12-02

Peptides

N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2

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