SMTL ID : 6wmm.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 1.55 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-BMA.1: 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.89, A:D.85 Hydrophobic interactions: A:Y.89 NAG-NAG-BMA.2: 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.95 Hydrogen bonds: B:D.85, B:Y.95

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.214, H.343 Ligands: UDP.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.214, A:H.343, H2O.1, H2O.6 MG.10: 3 residues within 4Å: Chain B: D.214, H.343 Ligands: UDP.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.214, B:H.343, H2O.9, H2O.15

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

UDP.4: 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.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.118 Hydrogen bonds: A:H.121, A:D.182, A:D.213, A:D.213 Water bridges: A:F.184, A:D.212 Salt bridges: A:K.255, A:K.255, A:H.343 pi-Stacking: A:F.184 UDP.11: 16 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, D.214, K.255, Y.256, H.343 Ligands: MG.10 14 PLIP interactions: 14 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, B:Y.256, B:Y.256 Water bridges: B:F.184, B:D.214 Salt bridges: B:K.255, B:K.255, B:H.343 pi-Stacking: B:F.184

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

NAG.5: 4 residues within 4Å: Chain A: N.61, C.63, N.94, Y.95 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.95 Hydrogen bonds: A:N.94 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.94 Water bridges: B:S.96

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

EDO.6: 5 residues within 4Å: Chain A: D.236, L.237, F.238, V.313, E.315 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.238 EDO.7: 7 residues within 4Å: Chain A: D.160, L.161, S.162, D.163 Chain B: Q.126, K.171, H.172 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.162, A:S.162, A:D.163, A:D.163, B:H.172 EDO.9: 4 residues within 4Å: Chain A: Y.287, H.288, T.290, D.291 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.287, A:T.290, A:T.290, A:D.291 Water bridges: A:D.291 EDO.14: 6 residues within 4Å: Chain B: Y.225, K.233, I.239, E.315, K.316, H.317 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.233, B:E.315 EDO.15: 5 residues within 4Å: Chain B: D.236, L.237, F.238, V.313, E.315 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.236, B:F.238 Water bridges: B:E.315

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.8: 7 residues within 4Å: Chain A: H.121, F.122, A.123, R.124, P.347 Chain B: K.346 Ligands: EPE.13 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:P.120, A:A.123, A:R.124, B:K.346, B:K.346 Water bridges: A:F.122, A:F.122 Salt bridges: A:R.124 EPE.13: 6 residues within 4Å: Chain B: H.121, F.122, A.123, R.124, P.347 Ligands: EPE.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.123, B:R.124 Water bridges: B:F.122 Salt bridges: B:R.124

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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