SMTL ID : 5fv9.2 (3 other biounits)

Crystal structure of GalNAc-T2 in complex with compound 16d

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

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

UDP.1: 14 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, H.359, R.362 Ligands: MN.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.143 Hydrogen bonds: A:D.176, A:D.176, A:R.201, A:S.207 Water bridges: A:H.145, A:E.147, A:R.362, A:R.362, A:R.362, A:R.362 Salt bridges: A:H.226, A:H.226, A:H.359, A:R.362 UDP.10: 14 residues within 4Å: Chain B: T.143, F.144, H.145, D.176, R.201, L.204, D.224, H.226, V.330, E.334, H.359, R.362 Ligands: Y6W.8, MN.9 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:T.143, B:L.204 Hydrogen bonds: B:D.176, B:R.201 Water bridges: B:L.204, B:L.204 Salt bridges: B:H.226, B:H.226, B:H.359, B:R.362

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

MN.2: 4 residues within 4Å: Chain A: D.224, H.226, H.359 Ligands: UDP.1 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: Y6W.8, UDP.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.224, B:H.226, B:H.359

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

EDO.3: 3 residues within 4Å: Chain A: G.535, S.536, N.537 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.537 EDO.4: 3 residues within 4Å: Chain A: Y.177, S.178, N.179 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.177, A:N.179 EDO.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.11: 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.12: 5 residues within 4Å: Chain B: E.481, A.483, K.491, H.492, M.493 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.438, B:E.481, B:M.493

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: Y.99, K.103, M.258 No protein-ligand interaction detected (PLIP) GOL.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 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.8: 16 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, V.330, E.334, H.359, R.362 Ligands: MN.9, UDP.10 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.143, B:L.204 Hydrogen bonds: B:D.176, B:R.201, B:S.207, B:E.334, B:R.362 Water bridges: B:L.204, B:L.204, B:S.225, B:A.307, B:G.309, B:E.334

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
A

B
B

GALNAC-T2

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