SMTL ID : 4d0t.1 (2 other biounits)

GalNAc-T2 crystal soaked with UDP-GalNAc, EA2 peptide and manganese

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

1 x ASP- SER- THR- THR- PRO- ALA- PRO: PEPTIDE(Non-covalent)

ASP-SER-THR-THR-PRO-ALA-PRO.1: 19 residues within 4Å: Chain A: I.253, V.255, L.270, F.280, W.282, A.307, W.331, F.361, R.362, K.363, H.365, S.373, G.374, F.377 Chain B: F.463, A.464 Ligands: UDP.3, EDO.4, NGA.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.270, A:F.361 Hydrogen bonds: A:A.307, A:R.362, A:S.373 Water bridges: A:R.362, A:A.378

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

MN.2: 4 residues within 4Å: Chain A: D.224, H.226, H.359 Ligands: UDP.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.224, A:H.226, A:H.359, H2O.2 MN.6: 4 residues within 4Å: Chain B: D.224, H.226, H.359 Ligands: UD2.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.224, B:H.226, B:H.359

1 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.3: 19 residues within 4Å: Chain A: T.143, F.144, H.145, D.176, R.201, G.203, L.204, D.224, S.225, H.226, V.330, W.331, H.359, R.362, Y.367 Ligands: ASP-SER-THR-THR-PRO-ALA-PRO.1, ASP-SER-THR-THR-PRO-ALA-PRO.1, MN.2, NGA.8 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:T.143, A:H.145, A:D.176, A:D.176, A:R.201, A:S.225, A:S.225, A:S.225, A:W.331, A:Y.367 Water bridges: A:R.362, A:R.362, A:R.362, A:R.362, A:R.362 Salt bridges: A:H.226, A:H.359, A:R.362 pi-Stacking: A:Y.367

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain A: V.279, F.280, N.335, F.377 Ligands: ASP-SER-THR-THR-PRO-ALA-PRO.1, NGA.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.278, A:F.280 EDO.5: 5 residues within 4Å: Chain A: P.165, H.166, I.168, K.169, K.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.169 Water bridges: A:K.192

1 x UD2: URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE(Non-covalent)

UD2.7: 23 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.307, G.308, G.309, L.310, V.330, W.331, G.332, E.334, H.359, R.362, Y.367 Ligands: MN.6 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:L.310 Hydrogen bonds: B:H.145, B:D.176, B:R.201, B:R.208, B:R.208, B:D.224, B:S.225, B:S.225, B:S.225, B:G.308, B:G.309, B:W.331, B:G.332, B:G.332 Salt bridges: B:H.226, B:H.359, B:R.362 pi-Stacking: B:Y.367

1 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Non-covalent)

NGA.8: 14 residues within 4Å: Chain A: L.204, R.208, D.224, A.307, G.308, G.309, W.331, G.332, E.334, N.335, H.359 Ligands: ASP-SER-THR-THR-PRO-ALA-PRO.1, UDP.3, EDO.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.208, A:R.208, A:D.224, A:G.308, A:G.309, A:G.332, A:E.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lira-Navarrete, E. et al., Substrate-Guided Front-Face Reaction Revealed by Combined Structural Snapshots and Metadynamics for the Polypeptide N-Acetylgalactosaminyltransferase 2. Angew.Chem.Int.Ed.Engl. (2014)

Release Date

2014-05-28

Peptides

POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
F

POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2

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