SMTL ID : 7s6n.1

N-acetylglucosamine-1-phosphotransferase (GNPT) alpha and beta subunits (GNPTAB) catalytic domain, from zebrafish

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

1 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.1: 9 residues within 4Å: Chain A: W.53, N.55, T.57, D.58, P.59, I.132, P.133, S.134, W.135 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.134, A:S.134

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.2: 6 residues within 4Å: Chain A: K.72, N.154, T.156, H.157, S.269, R.271 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.154, A:S.269 Water bridges: A:N.154, A:N.154

1 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.3: 11 residues within 4Å: Chain B: W.53, N.55, T.57, D.58, P.59, I.132, P.133, S.134, W.135, R.476, L.480 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.57 Hydrogen bonds: B:R.476, B:R.476

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.4: 6 residues within 4Å: Chain B: N.154, T.156, H.157, S.269, H.270, R.271 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.269

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

NAG.5: 4 residues within 4Å: Chain A: S.336, Q.339, M.340, N.343 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.339 Hydrogen bonds: A:N.343 NAG.6: 4 residues within 4Å: Chain A: N.296, S.298, E.299, D.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.296, A:S.298 NAG.7: 3 residues within 4Å: Chain A: N.416, S.418, H.419 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:H.419 Hydrogen bonds: A:S.418 NAG.9: 5 residues within 4Å: Chain B: Q.294, N.296, S.298, E.299, D.302 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.299 NAG.10: 3 residues within 4Å: Chain B: N.416, S.418, H.419 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.416

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 7 residues within 4Å: Chain A: D.305, D.307, S.309, V.311, L.312, S.313, E.316 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.305, A:S.309, A:V.311, A:E.316, H2O.1 CA.11: 7 residues within 4Å: Chain B: D.305, D.307, S.309, V.311, L.312, S.313, E.316 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.305, B:S.309, B:V.311, B:E.316, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorelik, A. et al., Structures of the mannose-6-phosphate pathway enzyme, GlcNAc-1-phosphotransferase. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-05-25

Peptides

N-acetylglucosamine-1-phosphotransferase (GNPT) alpha (GNPTAB) catalytic domain,N-acetylglucosamine-1-phosphotransferase subunit beta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-acetylglucosamine-1-phosphotransferase (GNPT) alpha (GNPTAB) catalytic domain,N-acetylglucosamine-1-phosphotransferase subunit beta

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