SMTL ID : 4d11.1 (3 other biounits)

GalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 peptide and manganese (Lower resolution dataset)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-dimer

Ligands

2 x SER- THR- CYS- PRO- ALA- ALA: PEPTIDE(Non-covalent)

SER-THR-CYS-PRO-ALA-ALA.1: 15 residues within 4Å: Chain A: F.463, A.464 Chain B: I.253, V.255, A.266, S.267, L.270, F.280, W.282, F.361, R.362, K.363, Q.364, H.365 Ligands: UDP.8 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.255, B:A.266, B:F.361, B:F.361, B:F.361 Hydrogen bonds: B:S.267, B:R.362, B:H.365, A:A.464, A:A.464 SER-THR-CYS-PRO-ALA-ALA.2: 14 residues within 4Å: Chain A: I.253, A.266, S.267, F.280, W.282, W.331, F.361, R.362, K.363, Q.364, H.365 Chain B: F.463, A.464 Ligands: UDP.5 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.266, A:F.361 Hydrogen bonds: A:S.267, A:R.362, A:H.365, B:A.464

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

MN.3: 4 residues within 4Å: Chain A: D.224, H.226, H.359 Ligands: UDP.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: UDP.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.224, B:H.226, B:H.359

2 x BBK: 2-acetamido-2-deoxy-5-thio-alpha-D-galactopyranose(Non-covalent)

BBK.4: 10 residues within 4Å: Chain A: D.458, L.460, G.461, Y.471, H.474, G.478, N.479 Chain B: H.474, A.476 Ligands: BBK.7 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:H.474 Hydrogen bonds: B:H.474, A:D.458, A:L.460, A:N.479, A:N.479 BBK.7: 9 residues within 4Å: Chain A: H.474, A.476 Chain B: D.458, L.460, Y.471, H.474, G.478, N.479 Ligands: BBK.4 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.458, B:L.460, B:N.479, B:N.479, B:Q.480 Hydrophobic interactions: A:H.474

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

UDP.5: 18 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, W.331, H.359, R.362, H.365, Y.367 Ligands: SER-THR-CYS-PRO-ALA.2, SER-THR-CYS-PRO-ALA.2, MN.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:H.145, A:D.176, A:R.201, A:S.225, A:S.225, A:S.225 Salt bridges: A:H.226, A:H.359, A:R.362, A:H.365, A:H.365 pi-Stacking: A:Y.367 UDP.8: 16 residues within 4Å: Chain B: T.143, F.144, H.145, D.176, R.201, G.203, L.204, D.224, S.225, H.226, H.359, R.362, H.365 Ligands: SER-THR-CYS-PRO-ALA-ALA.1, SER-THR-CYS-PRO-ALA-ALA.1, MN.6 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:H.145, B:D.176, B:D.176, B:R.201, B:L.204, B:S.225, B:S.225, B:S.225 Salt bridges: B:H.226, B:H.359, B:R.362, B:H.365, B:H.365

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 GALNAC-TRANSFERASE T2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

POLYPEPTIDE GALNAC-TRANSFERASE T2

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