SMTL ID : 5mu1.1

UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum soaked with K2PtI6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.48 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-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-MAN-MAN.1: 3 residues within 4Å: Chain A: N.618, S.620, M.621 No protein-ligand interaction detected (PLIP)

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.2: 3 residues within 4Å: Chain A: G.320, N.321, N.874 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: 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.3: 7 residues within 4Å: Chain A: N.36, T.38, I.39, D.72, G.73, H.74, E.658 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.4: 1 residues within 4Å: Chain A: N.1207 No protein-ligand interaction detected (PLIP)

14 x IOD: IODIDE ION(Non-functional Binders)

IOD.5: 3 residues within 4Å: Chain A: H.562 Ligands: IOD.6, PT.8 Ligand excluded by PLIP IOD.6: 4 residues within 4Å: Chain A: H.562 Ligands: IOD.5, IOD.7, PT.8 Ligand excluded by PLIP IOD.7: 4 residues within 4Å: Chain A: H.562, H.566 Ligands: IOD.6, PT.8 Ligand excluded by PLIP IOD.10: 5 residues within 4Å: Chain A: F.859, E.1022, H.1024, H.1247 Ligands: PT.9 Ligand excluded by PLIP IOD.11: 4 residues within 4Å: Chain A: F.614, M.616 Ligands: IOD.12, PT.14 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain A: Q.610 Ligands: IOD.11, IOD.13, PT.14 Ligand excluded by PLIP IOD.13: 5 residues within 4Å: Chain A: A.611, M.616, F.626 Ligands: IOD.12, PT.14 Ligand excluded by PLIP IOD.15: 4 residues within 4Å: Chain A: R.595, N.598, H.599 Ligands: PT.17 Ligand excluded by PLIP IOD.16: 3 residues within 4Å: Chain A: H.599, M.602 Ligands: PT.17 Ligand excluded by PLIP IOD.18: 4 residues within 4Å: Chain A: H.436, M.602 Ligands: IOD.19, PT.21 Ligand excluded by PLIP IOD.19: 5 residues within 4Å: Chain A: H.436, N.598 Ligands: IOD.18, IOD.20, PT.21 Ligand excluded by PLIP IOD.20: 7 residues within 4Å: Chain A: H.436, G.437, N.598, L.601, M.602 Ligands: IOD.19, PT.21 Ligand excluded by PLIP IOD.22: 4 residues within 4Å: Chain A: M.1316, N.1419, M.1421 Ligands: PT.24 Ligand excluded by PLIP IOD.23: 5 residues within 4Å: Chain A: E.1315, M.1316, Y.1319, M.1421 Ligands: PT.24 Ligand excluded by PLIP

6 x PT: PLATINUM (II) ION(Non-covalent)

PT.8: 4 residues within 4Å: Chain A: H.562 Ligands: IOD.5, IOD.6, IOD.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.562, A:H.562 PT.9: 5 residues within 4Å: Chain A: I.858, F.859, H.1024, H.1247 Ligands: IOD.10 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.1024, A:H.1247 PT.14: 4 residues within 4Å: Chain A: M.616 Ligands: IOD.11, IOD.12, IOD.13 No protein-ligand interaction detected (PLIP) PT.17: 3 residues within 4Å: Chain A: H.599 Ligands: IOD.15, IOD.16 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.599 PT.21: 5 residues within 4Å: Chain A: H.436, M.602 Ligands: IOD.18, IOD.19, IOD.20 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.436 PT.24: 4 residues within 4Å: Chain A: M.1316, M.1421 Ligands: IOD.22, IOD.23 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.25: 3 residues within 4Å: Chain A: D.1282, D.1284, D.1415 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.1282, A:D.1284, A:D.1284, A:D.1415

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roversi, P. et al., Interdomain conformational flexibility underpins the activity of UGGT, the eukaryotic glycoprotein secretion checkpoint. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-07-26

Peptides

UDP-glucose-glycoprotein glucosyltransferase-like protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-glucose-glycoprotein glucosyltransferase-like protein

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