SMTL ID : 5ajp.1

Crystal structure of the active form of GalNAc-T2 in complex with UDP and the glycopeptide MUC5AC-13

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-1-1-mer

Ligands

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

UDP.1: 18 residues within 4Å: Chain A: T.143, F.144, H.145, D.176, R.201, G.203, L.204, D.224, S.225, H.226, V.330, W.331, H.359, R.362, Y.367 Chain B: P.5, S.6 Ligands: MN.3 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.367 Hydrogen bonds: A:T.143, A:H.145, A:D.176, A:D.176, A:R.201, A:S.225, A:S.225, A:S.225, B:S.6, B:S.6 Water bridges: A:R.362, A:R.362, A:R.362, A:R.362 Salt bridges: A:H.226, A:H.359, A:R.362

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

SO4.2: 3 residues within 4Å: Chain A: V.500, D.501, R.502 Ligand excluded by PLIP SO4.4: 7 residues within 4Å: Chain A: H.145, N.146, N.179, R.201, Y.367, T.368 Ligands: SO4.22 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: E.243, D.244, R.245 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: I.525, E.526, G.527 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: H.123, R.293, P.297, R.356 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: E.191, K.192, V.193 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: L.196, R.210, A.214 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain A: R.132, V.133, D.134 Ligands: SO4.11 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain A: R.132 Ligands: SO4.10 Ligand excluded by PLIP SO4.12: 1 residues within 4Å: Chain A: R.543 Ligand excluded by PLIP SO4.13: 1 residues within 4Å: Chain A: R.77 Ligand excluded by PLIP SO4.14: 1 residues within 4Å: Chain A: R.543 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain A: R.240, R.247, K.302 Ligand excluded by PLIP SO4.16: 1 residues within 4Å: Chain A: K.546 Ligand excluded by PLIP SO4.17: 1 residues within 4Å: Chain A: R.532 Ligand excluded by PLIP SO4.18: 5 residues within 4Å: Chain A: Y.367, T.368, F.369, G.372, S.373 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain A: C.513, R.514, E.515 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain A: R.382, Y.408 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain A: P.401, N.528, K.564, N.568 Ligand excluded by PLIP SO4.22: 6 residues within 4Å: Chain A: H.145, Y.177, R.201, T.368, P.370 Ligands: SO4.4 Ligand excluded by PLIP SO4.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

MN.3: 4 residues within 4Å: Chain A: D.224, H.226, H.359 Ligands: UDP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.224, A:H.226, A:H.359, H2O.10

1 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Post Translational Modification)

A2G.24: 12 residues within 4Å: Chain A: D.458, L.460, G.461, Y.471, H.474, G.478, N.479, Q.480 Chain B: S.12, T.14, S.15, A.16 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.458, A:L.460, A:H.474, A:N.479, A:N.479, A:Q.480, B:S.12, B:S.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lira-Navarrete, E. et al., Dynamic Interplay between Catalytic and Lectin Domains of Galnac-Transferases Modulates Protein O-Glycosylation. Nat.Commun. (2015)

Release Date

2015-03-11

Peptides

POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2: A
MUCIN: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2

MUCIN

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