SMTL ID : 6nqt.2 (2 other biounits)

GalNac-T2 soaked with UDP-sugar

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

homo-dimer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: D.224, H.226, H.359 Ligands: LR7.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.224, A:H.226, A:H.359 MN.3: 4 residues within 4Å: Chain B: D.224, H.226, H.359 Ligands: LR7.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.224, B:H.226, B:H.359

2 x LR7: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R},6~{R})-3-(hex-5-ynoylamino)-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl] hydrogen phosphate(Non-covalent)

LR7.2: 27 residues within 4Å: Chain A: T.143, F.144, H.145, D.176, R.201, G.203, L.204, R.208, D.224, S.225, H.226, C.227, A.253, A.307, G.308, G.309, A.310, V.330, W.331, E.334, N.335, V.357, H.359, F.361, R.362, Y.367 Ligands: MN.1 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:A.253, A:A.310, A:V.357, A:F.361, A:Y.367 Hydrogen bonds: A:H.145, A:D.176, A:D.176, A:R.201, A:L.204, A:R.208, A:S.225, A:S.225, A:G.309, A:E.334, A:E.334 Water bridges: A:N.335, A:H.365, A:H.365 Salt bridges: A:H.226, A:H.359, A:R.362 LR7.4: 24 residues within 4Å: Chain B: T.143, F.144, H.145, D.176, R.201, G.203, L.204, R.208, D.224, S.225, H.226, A.253, A.307, G.308, G.309, W.331, G.332, E.334, N.335, H.359, F.361, R.362, Y.367 Ligands: MN.3 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:D.176, B:A.253, B:A.307, B:F.361 Hydrogen bonds: B:H.145, B:R.201, B:G.203, B:R.208, B:R.208, B:S.225, B:S.225, B:S.225, B:A.307, B:E.334, B:R.362, B:Y.367 Water bridges: B:N.335 Salt bridges: B:H.226, B:H.359

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schumann, B. et al., Bump-and-Hole Engineering Identifies Specific Substrates of Glycosyltransferases in Living Cells. Mol.Cell (2020)

Release Date

2020-01-29

Peptides

Polypeptide N-acetylgalactosaminyltransferase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Polypeptide N-acetylgalactosaminyltransferase 2

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