- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.07 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)
- 2 x MN: MANGANESE (II) ION(Non-covalent)
MN.2: 5 residues within 4Å:- Chain A: D.224, H.226, H.359
- Ligands: UDP.1, Y6W.3
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:D.224, A:H.226, A:H.359
MN.9: 5 residues within 4Å:- Chain B: D.224, H.226, H.359
- Ligands: UDP.8, Y6W.10
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:D.224, B:H.226, B:H.359
- 2 x Y6W: [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl hydrogen (S)-{3-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]propyl}phosphonate(Non-covalent)
Y6W.3: 16 residues within 4Å:- Chain A: T.143, F.144, H.145, D.176, R.201, G.203, L.204, S.207, D.224, H.226, V.330, E.334, H.359, R.362
- Ligands: UDP.1, MN.2
9 PLIP interactions:9 interactions with chain A- Hydrophobic interactions: A:T.143
- Hydrogen bonds: A:D.176, A:D.176, A:R.201, A:S.207, A:E.334
- Water bridges: A:H.145, A:L.204, A:L.204
Y6W.10: 17 residues within 4Å:- Chain B: T.143, F.144, H.145, D.176, R.201, G.203, L.204, S.207, D.224, H.226, G.309, V.330, E.334, H.359, R.362
- Ligands: UDP.8, MN.9
8 PLIP interactions:8 interactions with chain B- Hydrophobic interactions: B:T.143
- Hydrogen bonds: B:D.176, B:D.176, B:R.201, B:L.204, B:S.207, B:G.308, B:E.334
- 7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.4: 6 residues within 4Å:- Chain A: R.197, N.198, D.199, R.200, E.202, R.210
8 PLIP interactions:8 interactions with chain A- Hydrogen bonds: A:D.199, A:D.199, A:R.200, A:R.200, A:E.202, A:E.202, A:R.210
- Water bridges: A:R.210
EDO.5: 2 residues within 4Å:- Chain A: W.343, N.432
No protein-ligand interaction detected (PLIP)EDO.6: 3 residues within 4Å:- Chain A: Y.177, S.178, N.179
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Y.177
EDO.7: 5 residues within 4Å:- Chain A: E.481, W.482, K.491, H.492, M.493
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.481, A:M.493
EDO.11: 4 residues within 4Å:- Chain B: R.502, S.536, N.537, L.538
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:R.502, B:R.502, B:N.537
EDO.12: 3 residues within 4Å:- Chain B: P.407, Y.408, G.409
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:Y.408, B:Y.408, B:G.409
EDO.13: 4 residues within 4Å:- Chain B: R.514, D.517, S.518, R.519
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:D.517, B:S.518, B:R.519
- 2 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ghirardello, M. et al., Glycomimetics Targeting Glycosyltransferases: Synthetic, Computational and Structural Studies of Less-Polar Conjugates. Chemistry (2016)
- Release Date
- 2016-03-09
- Peptides
- GALNAC-T2: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
EB
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.07 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)
- 2 x MN: MANGANESE (II) ION(Non-covalent)
- 2 x Y6W: [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl hydrogen (S)-{3-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]propyl}phosphonate(Non-covalent)
- 7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 2 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ghirardello, M. et al., Glycomimetics Targeting Glycosyltransferases: Synthetic, Computational and Structural Studies of Less-Polar Conjugates. Chemistry (2016)
- Release Date
- 2016-03-09
- Peptides
- GALNAC-T2: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
EB
F