SMTL ID : 7sj2.1

N-acetylglucosamine-1-phosphotransferase (GNPT) alpha and beta subunits (GNPTAB) catalytic domain, from zebrafish, in complex with uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) and magnesium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.1: 10 residues within 4Å: Chain A: W.53, N.55, T.57, D.58, P.59, D.103, I.132, P.133, S.134, W.135 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.134

2 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.2: 5 residues within 4Å: Chain A: N.154, T.156, H.157, S.269, R.271 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.5: 5 residues within 4Å: Chain B: N.154, T.156, H.157, S.269, R.271 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.269

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

NAG-FUC.3: 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

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.4: 12 residues within 4Å: Chain B: W.53, N.55, T.57, D.58, P.59, D.103, I.132, P.133, S.134, W.135, R.476, L.480 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.57

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

NAG.6: 5 residues within 4Å: Chain A: N.296, S.298, E.299, D.302, K.375 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.296, A:S.298, A:E.299, A:D.302 NAG.7: 3 residues within 4Å: Chain A: N.416, S.418, D.447 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.416 Water bridges: A:N.416, A:V.417 NAG.12: 5 residues within 4Å: Chain B: N.296, S.298, E.299, D.302, K.375 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.296, B:E.299, B:D.302, B:D.302 NAG.13: 3 residues within 4Å: Chain B: N.416, S.418, H.419 No protein-ligand interaction detected (PLIP)

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.2 CA.14: 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:D.307, B:S.309, B:E.316, H2O.20

4 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 3 residues within 4Å: Chain A: D.186, N.438 Ligands: UD1.11 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.186, H2O.2, H2O.7 MG.10: 3 residues within 4Å: Chain A: S.99, E.102, D.439 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain B: D.186, N.438 Ligands: UD1.17 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.186, H2O.19, H2O.22 MG.16: 4 residues within 4Å: Chain B: S.99, R.100, E.102 Ligands: UD1.17 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.102, H2O.18, H2O.19, H2O.19, H2O.21

2 x UD1: URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE(Non-covalent)

UD1.11: 24 residues within 4Å: Chain A: T.52, W.53, V.54, R.100, F.101, H.148, F.161, S.163, P.164, I.166, E.167, Y.182, N.184, D.185, D.186, V.187, H.243, M.244, H.246, R.273, Q.279, C.436, N.438 Ligands: MG.9 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:V.54, A:F.101, A:V.187 Hydrogen bonds: A:T.52, A:T.52, A:V.54, A:S.163, A:N.184, A:N.184, A:D.185, A:D.185, A:H.246, A:Q.279, A:N.438, A:N.438 Water bridges: A:W.53, A:W.53, A:R.100, A:D.186, A:R.273, A:R.273, A:D.439 Salt bridges: A:R.273, A:R.273, A:R.273 UD1.17: 25 residues within 4Å: Chain B: T.52, W.53, V.54, R.100, F.101, H.148, F.161, S.163, P.164, I.166, E.167, Y.182, N.184, D.185, D.186, V.187, H.243, M.244, H.246, R.273, Q.279, C.436, N.438 Ligands: MG.15, MG.16 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:F.101, B:V.187, B:H.243 Hydrogen bonds: B:T.52, B:T.52, B:V.54, B:R.100, B:S.163, B:N.184, B:N.184, B:D.185, B:Q.279, B:N.438, B:N.438 Water bridges: B:W.53, B:W.53, B:S.163, B:D.186, B:D.186, B:R.273 Salt bridges: B:R.273, B:R.273

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

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