SMTL ID : 6nqt.1 (2 other biounits)

GalNac-T2 soaked with UDP-sugar

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: D.224, H.226, H.359, R.362 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: 28 residues within 4Å: Chain A: T.143, F.144, H.145, E.147, 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, G.332, E.334, N.335, V.357, H.359, R.362, Y.367 Ligands: MN.1 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:A.253, A:A.310, A:V.357, A:H.359 Hydrogen bonds: A:H.145, A:E.147, A:D.176, A:D.176, A:R.201, A:R.201, A:L.204, A:R.208, A:R.208, A:S.225, A:S.225, A:S.225, A:G.309, A:G.332, A:E.334, A:E.334, A:R.362, A:Y.367 Water bridges: A:H.365 Salt bridges: A:H.226, A:H.359, A:R.362 pi-Stacking: A:Y.367 LR7.4: 26 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, P.251, A.307, G.308, G.309, A.310, V.330, W.331, G.332, E.334, N.335, V.357, H.359, R.362, Y.367 Ligands: MN.3 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:P.251, B:A.310, B:V.357, B:H.359 Hydrogen bonds: B:H.145, B:D.176, B:L.204, B:R.208, B:S.225, B:S.225, B:S.225, B:G.309, B:G.332, B:E.334, B:E.334 Water bridges: B:T.143 Salt bridges: B:H.226, B:H.359, B:R.362 pi-Stacking: B:Y.367

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
A

B
C

Polypeptide N-acetylgalactosaminyltransferase 2

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