SMTL ID : 5nqa.1 (1 other biounit)

Crystal structure of GalNAc-T4 in complex with the monoglycopeptide 3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: G.311, G.312, L.313, H.362, F.364 Ligands: EDO.12 Ligand excluded by PLIP EDO.2: 5 residues within 4Å: Chain A: G.245, R.246, D.247, E.248 Ligands: EDO.25 Ligand excluded by PLIP EDO.3: 8 residues within 4Å: Chain A: G.277, F.278, F.284, T.308, M.309, N.338, L.339, S.342 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: K.66, R.114, I.116, S.157, T.161, E.231, C.232 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: R.197, L.198, I.199, R.200 Ligands: EDO.10 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: R.99, D.178, R.179, V.180, Y.181 Ligand excluded by PLIP EDO.7: 1 residues within 4Å: Chain A: K.82 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: R.246 Ligands: EDO.33 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: K.119, E.265 Ligands: EDO.23 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: I.199, R.200, I.213 Ligands: EDO.5 Ligand excluded by PLIP EDO.11: 1 residues within 4Å: Chain A: N.466 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: L.207, G.311, G.312, N.338 Ligands: EDO.1, EDO.29 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: D.58, S.60, R.61, P.62, K.65 Ligand excluded by PLIP EDO.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: D.260, W.261, N.262 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: D.388, E.389, K.391 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: R.416, C.421, K.422, S.423 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: N.471, Y.551, D.559 Ligands: EDO.19 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: N.471, Y.512 Ligands: EDO.18, EDO.20 Ligand excluded by PLIP EDO.20: 1 residues within 4Å: Ligands: EDO.19 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain A: Y.551, P.554 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: E.242, R.243, R.246 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: K.119, M.268, I.270 Ligands: EDO.9, EDO.37 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain A: M.274 Ligands: EDO.36 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain A: P.135, D.221, I.244, G.245, E.248 Ligands: EDO.2 Ligand excluded by PLIP EDO.26: 1 residues within 4Å: Chain A: K.534 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain A: E.417, R.418, R.420 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain A: W.334, G.335, F.375 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain A: L.207, V.208, R.211, G.312, Y.327, E.337, N.338 Ligands: EDO.12 Ligand excluded by PLIP EDO.30: 7 residues within 4Å: Chain A: A.142, F.143, Y.144, D.175, R.204, G.206, L.207 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain A: R.246 Ligands: EDO.33, GOL.38 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain A: Y.488, K.492, H.532, F.533 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain A: I.298 Ligands: EDO.8, EDO.31, GOL.38 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain A: E.123, Q.127, S.299 Ligands: GOL.38 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain A: E.404, A.405, Y.406, G.407, D.408 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain A: E.272, M.274, S.288, R.294 Ligands: EDO.24, EDO.37 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain A: I.270 Ligands: EDO.23, EDO.36 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.38: 6 residues within 4Å: Chain A: I.298, S.299, D.302 Ligands: EDO.31, EDO.33, EDO.34 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.302 GOL.39: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.40: 2 residues within 4Å: Chain A: T.216, F.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.216 Water bridges: A:T.216 GOL.41: 3 residues within 4Å: Chain A: K.422, S.423, W.426 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.423, A:S.423 Water bridges: A:S.423, A:D.425, A:D.425 GOL.42: 2 residues within 4Å: Chain A: K.128, F.129 No protein-ligand interaction detected (PLIP) GOL.43: 1 residues within 4Å: Chain A: K.125 No protein-ligand interaction detected (PLIP)

1 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Non-covalent)

NGA.44: 9 residues within 4Å: Chain A: D.459, N.461, F.475, H.478, Q.480, G.481, G.482, N.483, Q.484 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Q.480 Hydrogen bonds: A:D.459, A:H.478, A:N.483, A:N.483, A:Q.484

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rivas, M.L. et al., The interdomain flexible linker of the polypeptide GalNAc transferases dictates their long-range glycosylation preferences. Nat Commun (2017)

Release Date

2017-12-20

Peptides

Polypeptide N-acetylgalactosaminyltransferase 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polypeptide N-acetylgalactosaminyltransferase 4

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