SMTL ID : 7s69.1

N-acetylglucosamine-1-phosphotransferase (GNPT) gamma subunit (GNPTG), from clawed frog

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.04 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN.1: 10 residues within 4Å: Chain A: L.35, P.37, G.55, K.56, C.57, C.70, H.73, N.74, T.76, I.90 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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-MAN-MAN-MAN-MAN-MAN.2: 10 residues within 4Å: Chain B: L.35, P.37, G.55, K.56, C.57, C.70, H.73, N.74, T.76, I.90 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.55

10 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: P.47, S.48, H.49, T.165 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: N.102 Chain B: H.158 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: Y.87, C.115, R.120 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: E.176 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: S.42, P.43, G.203, K.206 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: F.51, A.54 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: Y.182, E.184 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: L.181, E.188, H.191 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: K.66, E.68 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: R.110, Q.121 Ligand excluded by PLIP

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 gamma subunit: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-acetylglucosamine-1-phosphotransferase gamma subunit