SMTL ID : 6s22.1

Crystal structure of the TgGalNAc-T3 in complex with UDP, manganese and FGF23c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: P.169, I.172, E.173 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.173, A:E.173 EDO.2: 7 residues within 4Å: Chain A: F.176, K.177, C.179, P.180, L.182, A.290, A.293 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.177, A:K.177 EDO.3: 7 residues within 4Å: Chain A: W.397, Q.398, C.399, G.400, Q.479, K.481, W.485 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.479 Water bridges: A:G.400 EDO.4: 7 residues within 4Å: Chain A: F.329, D.330, W.331, Y.491, A.494, Y.495, Q.555 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.329, A:Y.495 Water bridges: A:Q.555 EDO.5: 5 residues within 4Å: Chain A: R.326, R.356, P.358, N.489, V.490 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.326, A:R.326, A:E.344 EDO.6: 4 residues within 4Å: Chain A: E.373, Y.374, L.474, R.477 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.374, A:R.477, A:R.477 Water bridges: A:G.376 EDO.7: 5 residues within 4Å: Chain A: Y.544, H.589, F.627 Ligands: EDO.9, EDO.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.589 EDO.8: 2 residues within 4Å: Ligands: EDO.9, EDO.11 No protein-ligand interaction detected (PLIP) EDO.9: 7 residues within 4Å: Chain A: H.589, Q.593, I.626, F.627 Ligands: EDO.7, EDO.8, EDO.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.589, A:Q.593, A:F.627 EDO.10: 3 residues within 4Å: Chain A: Y.506, K.508, C.533 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.508 EDO.11: 6 residues within 4Å: Chain A: H.589, Q.590, Q.593 Ligands: EDO.7, EDO.8, EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.593 EDO.12: 1 residues within 4Å: Chain A: N.117 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.117 EDO.13: 4 residues within 4Å: Chain A: E.447, Y.450, A.457, V.460 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.447, A:A.457 Water bridges: A:E.447 EDO.14: 4 residues within 4Å: Chain A: Q.174, R.291, E.294, T.352 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.174

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.15: 4 residues within 4Å: Chain A: Y.374, R.477, L.478, Q.479 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.374, A:R.477, A:Q.479

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

UDP.16: 16 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, W.385, H.413, R.416 Chain B: H.8, T.9 Ligands: MN.17 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:H.192, A:D.223, A:D.223, A:A.276, B:T.9 Water bridges: A:R.416, A:R.416 Salt bridges: A:H.277, A:H.413, A:R.416, B:H.8, B:H.8

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

MN.17: 4 residues within 4Å: Chain A: D.275, H.277, H.413 Ligands: UDP.16 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.275, A:H.277, A:H.413, H2O.7

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

NAG.18: 3 residues within 4Å: Chain A: E.444, N.482, W.485 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.482 Water bridges: A:E.444, A:E.444, A:E.444

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 7 residues within 4Å: Chain A: L.105, R.167, C.171, F.176, G.283, E.286, P.287 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.167, A:R.167, A:E.286, A:E.286

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

NGA.20: 12 residues within 4Å: Chain A: D.517, G.519, E.520, Y.531, H.534, L.536, G.538, N.539, Q.540 Chain B: T.2, P.3, I.4 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.536, B:I.4 Hydrogen bonds: A:D.517, A:G.519, 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
Fibroblast growth factor 23: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
F

Polypeptide N-acetylgalactosaminyltransferase

Fibroblast growth factor 23

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