SMTL ID : 5nqa.2 (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

hetero-1-1-mer

Ligands

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

EDO.1: 2 residues within 4Å: Chain A: E.242, R.246 Ligand excluded by PLIP EDO.2: 7 residues within 4Å: Chain A: L.207, V.208, R.211, G.312, Y.327, E.337, N.338 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: P.442, G.443, W.444, H.445, K.578 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: R.296, R.297, I.298, D.302, P.303 Ligands: EDO.26 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: I.244, G.245, R.246, D.247, E.248 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: I.298, S.299, D.302 Ligands: EDO.19 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: D.118, K.125, S.234 Ligand excluded by PLIP EDO.8: 1 residues within 4Å: Chain A: K.319 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: R.305, W.346, N.430 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: Q.322, Y.323, G.325, L.415 Ligands: EDO.28 Ligand excluded by PLIP EDO.11: 1 residues within 4Å: Chain A: T.216 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: H.287, N.434, L.435 Ligand excluded by PLIP EDO.13: 1 residues within 4Å: Ligands: EDO.21 Ligand excluded by PLIP EDO.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: I.256, G.311, G.312, L.313, H.362, F.364 Ligand excluded by PLIP EDO.16: 1 residues within 4Å: Ligands: EDO.34 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: M.274, W.286 Ligands: EDO.25 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: R.99, Y.100, R.179 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: E.123, Q.127, S.299 Ligands: EDO.6 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: K.128, F.129, N.130, R.132 Ligand excluded by PLIP EDO.21: 1 residues within 4Å: Ligands: EDO.13 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain A: N.130, T.133 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: F.143, Y.144, D.175, R.204, G.206, L.207 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain A: A.215, T.216, L.223, K.318, F.321, Q.322, T.326 Ligand excluded by PLIP EDO.25: 1 residues within 4Å: Ligands: EDO.17 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain A: R.243, R.246, D.302, P.303 Ligands: EDO.4 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain A: D.227, C.228, H.229, H.362 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain A: Q.322, Y.323 Ligands: EDO.10 Ligand excluded by PLIP EDO.29: 2 residues within 4Å: Chain A: R.441, S.490 Ligand excluded by PLIP EDO.30: 1 residues within 4Å: Chain A: R.300 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain A: P.442, G.443, W.444 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain A: S.71, A.73, G.75, E.76, K.79 Ligand excluded by PLIP EDO.33: 8 residues within 4Å: Chain A: P.67, P.68, A.69, E.76, S.111, H.113, R.114, H.115 Ligand excluded by PLIP EDO.34: 2 residues within 4Å: Chain A: R.418 Ligands: EDO.16 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.35: 4 residues within 4Å: Chain A: A.69, D.70, S.71, R.72 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.70, A:S.71, A:S.71 GOL.36: 3 residues within 4Å: Chain A: K.119, R.120, I.270 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.119, A:R.120, A:R.120, A:K.125 GOL.37: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.38: 3 residues within 4Å: Chain A: Q.292, D.295, R.296 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.292

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

NGA.39: 9 residues within 4Å: Chain A: D.459, N.461, F.475, H.478, Q.480, G.482, N.483, Q.484 Chain B: T.3 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Q.480 Hydrogen bonds: A:D.459, A:H.478, A:N.483, A:N.483, A:Q.484 Water bridges: A:H.478, B:T.3

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
Monoglycopeptide 3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
G

Polypeptide N-acetylgalactosaminyltransferase 4

Monoglycopeptide 3

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