SMTL ID : 6s24.1

Crystal structure of the TgGalNAc-T3 in complex with UDP, manganese and the peptide 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

hetero-1-1-mer

Ligands

1 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.1: 12 residues within 4Å: Chain A: R.259, D.275, I.304, A.361, G.362, G.363, L.364, H.413, F.415 Chain B: T.11 Ligands: UDP.17, MN.18 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.361, A:L.364 Hydrogen bonds: A:R.259, A:G.363, A:L.364, A:L.364, B:T.11

16 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: H.192, N.193, V.226, R.252, T.422 Ligand excluded by PLIP PO4.3: 5 residues within 4Å: Chain A: P.183, E.269, T.270, I.292, S.368 Ligand excluded by PLIP PO4.4: 3 residues within 4Å: Chain A: R.291, E.294, N.295 Ligand excluded by PLIP PO4.5: 2 residues within 4Å: Chain A: E.338, S.339 Ligand excluded by PLIP PO4.6: 3 residues within 4Å: Chain A: H.561, Q.568, R.570 Ligand excluded by PLIP PO4.7: 2 residues within 4Å: Chain A: R.570, E.571 Ligand excluded by PLIP PO4.8: 2 residues within 4Å: Chain A: R.451, S.504 Ligand excluded by PLIP PO4.9: 3 residues within 4Å: Chain A: D.498, L.499, N.500 Ligand excluded by PLIP PO4.10: 7 residues within 4Å: Chain A: D.498, S.545, A.546, H.547, E.549, R.551, Y.574 Ligand excluded by PLIP PO4.11: 4 residues within 4Å: Chain A: F.503, Y.544, H.589, F.627 Ligand excluded by PLIP PO4.12: 4 residues within 4Å: Chain A: N.607, G.608, E.609, H.610 Ligand excluded by PLIP PO4.13: 3 residues within 4Å: Chain A: V.582, G.583, A.599 Ligand excluded by PLIP PO4.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PO4.15: 2 residues within 4Å: Chain A: T.101, R.178 Ligand excluded by PLIP PO4.16: 2 residues within 4Å: Chain A: S.157, H.159 Ligand excluded by PLIP PO4.21: 4 residues within 4Å: Chain A: S.306, F.415 Chain B: G.13, P.14 Ligand excluded by PLIP

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

UDP.17: 19 residues within 4Å: Chain A: V.190, F.191, H.192, D.223, R.252, G.254, L.255, D.275, A.276, H.277, I.384, W.385, H.413, R.416, H.421 Chain B: T.10, T.11 Ligands: TAM.1, MN.18 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.192, A:D.223, A:D.223, A:R.252, A:A.276, B:T.11 Water bridges: A:R.416, A:R.416 Salt bridges: A:H.277, A:H.413, A:R.416, A:H.421

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

MN.18: 5 residues within 4Å: Chain A: D.275, H.277, H.413 Ligands: TAM.1, UDP.17 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.275, A:H.277, A:H.413, H2O.4

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.19: 2 residues within 4Å: Chain A: N.482, W.485 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.482

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

NGA.20: 11 residues within 4Å: Chain A: D.517, G.519, E.520, Y.531, H.534, G.538, N.539, Q.540 Chain B: T.2, G.3, A.4 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.517, A:E.520, A:H.534, A:N.539, A:N.539, A:Q.540, B:T.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Las Rivas, M. et al., Molecular basis for fibroblast growth factor 23 O-glycosylation by GalNAc-T3. Nat.Chem.Biol. (2020)

Release Date

2019-12-25

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
F

Polypeptide N-acetylgalactosaminyltransferase

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

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