SMTL ID : 7q4i.1

Crystal structure of DmC1GalT1 in complex with UDP-Mn2+ and the APD-TGalNAc-RP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x ALA- PRO- ASP- THR- ARG- LPD: Mucin-1(Non-covalent)

ALA-PRO-ASP-THR-ARG-LPD.1: 10 residues within 4Å: Chain B: R.80, Y.141, F.212, H.222, F.227, W.228, Y.232, Y.253 Ligands: UDP.6, A2G.9 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.228 Hydrogen bonds: B:Y.253 ALA-PRO-ASP-THR-ARG-LPD.2: 8 residues within 4Å: Chain A: R.80, Y.141, W.228, Y.232, Y.253 Ligands: UDP.3, EDO.10, A2G.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.228, A:Y.232 Water bridges: A:Y.253

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

UDP.3: 17 residues within 4Å: Chain A: M.34, T.35, N.36, N.39, E.78, G.79, R.80, L.83, K.86, D.109, D.110, D.111, H.252, Y.253 Ligands: ALA-PRO-ASP-THR-ARG-LPD.2, MN.5, EDO.10 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:R.80 Hydrogen bonds: A:N.36, A:N.39, A:E.78, A:E.78, A:G.79, A:D.110, A:D.110 Water bridges: A:K.43, A:D.111 Salt bridges: A:K.43, A:R.80, A:R.80, A:H.252 UDP.6: 16 residues within 4Å: Chain B: M.34, T.35, N.36, N.39, E.78, G.79, R.80, L.83, K.86, D.109, D.110, D.111, H.252, Y.253 Ligands: ALA-PRO-ASP-THR-ARG-LPD.1, MN.8 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:N.36, B:N.39, B:E.78, B:E.78, B:G.79, B:D.110, B:D.110, B:Y.253 Water bridges: B:K.43, B:D.111 Salt bridges: B:K.43, B:R.80, B:R.80, B:H.252

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

EDO.4: 2 residues within 4Å: Chain A: Y.95, R.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.161 EDO.7: 7 residues within 4Å: Chain A: L.265, I.266, L.269 Chain B: L.265, I.266, L.269, R.270 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.265 EDO.10: 3 residues within 4Å: Ligands: ALA-PRO-ASP-THR-ARG-LPD.2, ALA-PRO-ASP-THR-ARG-LPD.2, UDP.3 No protein-ligand interaction detected (PLIP)

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

MN.5: 4 residues within 4Å: Chain A: D.109, D.111, H.252 Ligands: UDP.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.109, A:D.111, A:D.111, A:H.252 MN.8: 4 residues within 4Å: Chain B: D.109, D.111, H.252 Ligands: UDP.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.109, B:D.111, B:D.111, B:H.252

2 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.9: 10 residues within 4Å: Chain B: F.138, Y.141, Y.146, S.148, D.183, V.184, P.211, Y.232 Ligands: ALA-PRO-ASP-THR-ARG-LPD.1, ALA-PRO-ASP-THR-ARG-LPD.1 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.211 Hydrogen bonds: B:Y.141, B:Y.141, B:Y.146, B:D.183, B:Y.232 A2G.11: 11 residues within 4Å: Chain A: F.138, Y.141, Y.146, S.148, A.181, D.183, V.184, W.228, Y.232 Ligands: ALA-PRO-ASP-THR-ARG-LPD.2, ALA-PRO-ASP-THR-ARG-LPD.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.183, A:Y.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gonzalez-Ramirez, A.M. et al., Structural basis for the synthesis of the core 1 structure by C1GalT1. Nat Commun (2022)

Release Date

2022-04-13

Peptides

Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1