SMTL ID : 4d0t.2 (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 THR- THR- PRO- ALA- PRO- THR: PEPTIDE(Non-covalent)

THR-THR-PRO-ALA-PRO-THR.1: 19 residues within 4Å: Chain A: P.251, I.252, I.253, V.255, A.266, S.267, L.270, F.280, W.282, W.331, H.359, F.361, R.362, K.363, Q.364, H.365 Chain B: F.463, A.464 Ligands: UD2.5 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.255, A:A.266, A:L.270, A:W.282, A:F.361, A:F.361, B:A.464 Hydrogen bonds: A:I.253, A:I.253, A:S.267 Water bridges: A:L.270

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

MN.2: 4 residues within 4Å: Chain A: D.224, H.226, H.359 Ligands: UD2.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.224, A:H.226, A:H.359 MN.6: 4 residues within 4Å: Chain B: D.224, H.226, H.359 Ligands: UD2.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.224, B:H.226, B:H.359, H2O.6

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

EDO.3: 2 residues within 4Å: Chain A: E.231, H.232 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.231 EDO.4: 4 residues within 4Å: Chain A: R.543, A.558, L.559, S.560 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.543, A:L.559, A:S.560, A:S.560 EDO.8: 4 residues within 4Å: Chain B: D.80, F.81, N.82, K.189 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.82, B:N.82, B:K.189 EDO.9: 6 residues within 4Å: Chain B: R.132, D.134, L.135, P.136, K.218, A.242 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.132, B:R.132, B:D.134, B:K.218, B:K.218

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

UD2.5: 25 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, A.307, G.308, G.309, L.310, V.330, W.331, G.332, E.334, H.359, R.362, Y.367 Ligands: THR-THR-PRO-ALA-PRO-THR.1, THR-THR-PRO-ALA-PRO-THR.1, MN.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.310 Hydrogen bonds: A:H.145, A:D.176, A:R.201, A:R.208, A:R.208, A:D.224, A:S.225, A:S.225, A:S.225, A:G.308, A:G.309, A:W.331, A:G.332, A:E.334 Salt bridges: A:H.226, A:H.359, A:R.362 pi-Stacking: A:Y.367 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 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:L.310 Hydrogen bonds: B:T.143, B:H.145, B:D.176, B:D.176, B:R.201, B:G.203, 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:E.334, B:Y.367 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

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
B

B
E

POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2

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