SMTL ID : 5ajn.1

Crystal structure of the inactive form of GalNAc-T2 in complex with the glycopeptide MUC5AC-Cys13

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

hetero-1-1-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: K.363, Q.364, H.365 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.364, A:H.365 Water bridges: A:K.363 Salt bridges: A:K.363 SO4.2: 2 residues within 4Å: Chain A: R.382, Y.408 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.404, A:Y.408 Water bridges: A:R.382, A:R.382, A:R.382 Salt bridges: A:R.382 SO4.3: 2 residues within 4Å: Chain A: A.117, K.161 8 PLIP interactions: 8 interactions with chain A Water bridges: A:I.118, A:K.161, A:K.161, A:K.161, A:K.161, A:K.162 Salt bridges: A:K.161, A:K.162 SO4.4: 3 residues within 4Å: Chain A: R.113, R.116, A.117 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.117 Water bridges: A:R.113, A:D.115, A:D.115 SO4.5: 2 residues within 4Å: Chain A: G.88, G.89 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.89 Water bridges: A:A.85, A:R.149, A:R.149, A:R.149 SO4.6: 1 residues within 4Å: Chain A: R.532 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.532 SO4.7: 1 residues within 4Å: Chain A: R.543 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.560 Salt bridges: A:R.543 SO4.8: 4 residues within 4Å: Chain A: H.123, R.293, Q.294, P.297 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.294, A:Q.294 Water bridges: A:R.293 Salt bridges: A:R.293 SO4.9: 9 residues within 4Å: Chain A: H.226, H.359, V.360, F.361, R.362 Chain B: T.2, T.3, P.4, S.5 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.2, B:T.2, B:S.5, A:R.362 Salt bridges: A:H.226, A:H.359, A:R.362 SO4.10: 2 residues within 4Å: Chain A: E.526, G.527 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.526, A:G.527 Water bridges: A:I.525 SO4.11: 1 residues within 4Å: Chain A: R.543 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.543 SO4.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

EDO.12: 4 residues within 4Å: Chain A: P.136, A.137, H.166, K.218 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.137, A:H.166 EDO.13: 4 residues within 4Å: Chain A: P.370, V.400, P.401, S.402 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.402, A:S.402 Water bridges: A:S.402, A:K.564 EDO.14: 3 residues within 4Å: Chain A: Y.367, T.368, S.373 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.368, A:S.373 Water bridges: A:K.363, A:P.366, A:G.372 EDO.15: 6 residues within 4Å: Chain A: P.251, I.252, I.253, A.266, W.282 Chain B: P.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.251, A:I.253 Water bridges: A:A.266 EDO.16: 2 residues within 4Å: Chain A: A.299, P.300 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.240 Water bridges: A:R.240 EDO.17: 5 residues within 4Å: Chain A: S.542, R.543, T.544, A.545, K.546 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.546 EDO.18: 5 residues within 4Å: Chain A: Y.324, D.325, M.326, S.413, R.414 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.325, A:M.326, A:S.413, A:S.413, A:R.414 EDO.19: 4 residues within 4Å: Chain A: Q.452, S.542, L.559, S.560 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.455, A:L.559 EDO.20: 1 residues within 4Å: Chain A: R.201 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.201, A:R.201, A:W.331 Water bridges: A:H.145, A:N.146 EDO.21: 3 residues within 4Å: Chain A: A.117, I.118, P.119 No protein-ligand interaction detected (PLIP) EDO.22: 4 residues within 4Å: Chain A: D.244, T.246, R.247, K.302 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.246, A:T.246, A:R.247, A:K.302, A:K.302 EDO.23: 2 residues within 4Å: Chain A: L.196, R.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.210 Water bridges: A:R.210 EDO.24: 4 residues within 4Å: Chain A: E.526, G.527, S.529, K.564 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.529, A:S.529, A:K.564 EDO.26: 2 residues within 4Å: Chain A: R.438, M.493 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.438, A:R.438 Water bridges: A:M.493

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

A2G.25: 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.11, C.13, S.14, A.15 9 PLIP interactions: 7 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.11, B:S.11 Water bridges: A:Y.471

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
P

POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2

MUCIN

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