SMTL ID : 6h0b.2 (1 other biounit)

Crystal structure of the human GalNAc-T4 in complex with UDP, manganese and the diglycopeptide 6.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: D.227, H.229, H.362 Ligands: UDP.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.227, A:H.229, A:H.362, H2O.2

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

UDP.2: 19 residues within 4Å: Chain A: A.142, F.143, Y.144, D.175, R.204, G.206, L.207, A.210, D.227, C.228, H.229, V.333, W.334, H.362, Y.370, R.372 Chain B: T.12 Ligands: MN.1, EDO.3 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.207, A:Y.370 Hydrogen bonds: A:Y.144, A:D.175, A:D.175, A:R.204, A:R.204, A:G.206, A:C.228, A:Y.370, B:T.12 Water bridges: A:R.372, A:R.372, B:T.12 Salt bridges: A:H.229, A:H.362, A:R.372, A:R.372

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

EDO.3: 9 residues within 4Å: Chain A: D.227, A.310, G.311, G.312, L.313, H.362, F.364 Chain B: T.12 Ligands: UDP.2 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: W.77, K.79, E.117 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain A: R.197, L.198 Ligand excluded by PLIP EDO.6: 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.7: 3 residues within 4Å: Chain A: E.94, I.97, E.98 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: T.136, A.164, V.165, K.168, R.195 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: Y.189, N.192 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: H.287, S.288, P.290, N.434 Ligands: EDO.16 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: G.325, E.411, R.412 Ligand excluded by PLIP EDO.12: 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.13: 3 residues within 4Å: Chain A: R.305, W.426, N.430 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: D.260, W.261 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: Y.267, M.268, Q.269 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: H.287, F.432, N.434, L.435 Ligands: EDO.10 Ligand excluded by PLIP EDO.17: 1 residues within 4Å: Chain A: R.296 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain A: E.265, Y.267 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain A: D.108, W.148 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: H.436, E.439, T.489, N.491, E.493, R.495 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 3 residues within 4Å: Chain A: E.272, M.274, S.288 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Q.269, A:E.272, A:M.274, A:V.289

2 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Post Translational Modification)

NGA.22: 8 residues within 4Å: Chain A: R.281, T.283, Q.285, K.366, R.367 Chain B: T.11, T.12, P.13 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:T.11, A:Q.285, A:K.366 Water bridges: B:T.11, A:R.281, A:R.281 Hydrophobic interactions: A:T.283 NGA.23: 11 residues within 4Å: Chain A: D.459, N.461, F.475, H.478, Q.480, G.482, N.483, Q.484 Chain B: A.2, T.3, G.4 7 PLIP interactions: 6 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, B:A.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Las Rivas, M. et al., Structural and Mechanistic Insights into the Catalytic-Domain-Mediated Short-Range Glycosylation Preferences of GalNAc-T4. ACS Cent Sci (2018)

Release Date

2018-10-10

Peptides

Polypeptide N-acetylgalactosaminyltransferase 4: A
ALA-THR-GLY-ALA-GLY-ALA-GLY-ALA-GLY-THR-THR-PRO-GLY-PRO-GLY: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
F

Polypeptide N-acetylgalactosaminyltransferase 4

ALA-THR-GLY-ALA-GLY-ALA-GLY-ALA-GLY-THR-THR-PRO-GLY-PRO-GLY

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