SMTL ID : 8v9q.1

Crystal structure of mGalNAc-T1 in complex with the mucin glycopeptide Muc5AC-13, Mn2+, and UDP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

hetero-2-3-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 8 residues within 4Å: Chain A: E.416, R.426, H.427, Y.428, F.429, S.430, L.431, N.552 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.426, A:H.427, A:Y.428 Hydrophobic interactions: A:H.427

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 2 residues within 4Å: Chain A: N.95, S.97 No protein-ligand interaction detected (PLIP)

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

UDP.3: 20 residues within 4Å: Chain A: V.123, F.124, H.125, D.156, R.186, S.187, G.188, L.189, D.209, A.210, H.211, I.315, H.344, R.347, T.350, Y.352, F.354 Chain B: T.2, T.3 Ligands: MN.9 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.352 Hydrogen bonds: A:V.123, A:H.125, A:D.156, A:R.186, A:R.186, A:S.187, A:A.210, A:Y.352, B:T.3, B:T.3 Water bridges: A:H.125, A:H.211, A:R.347, A:R.347, A:R.347, A:R.347, A:R.347 Salt bridges: A:H.211, A:H.344, A:R.347 UDP.14: 17 residues within 4Å: Chain C: F.124, H.125, D.156, R.186, S.187, G.188, L.189, A.192, D.209, A.210, H.211, H.344, R.347, T.350 Chain D: T.2, T.3 Ligands: MN.17 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:F.124, C:D.156, C:A.210, D:T.3, D:T.3, D:T.3 Salt bridges: C:H.211, C:H.344, C:R.347, C:R.347 pi-Stacking: C:H.125

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: E.104, G.105, T.108, K.109, D.281, T.283, L.284 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.105, A:T.108, A:K.109, A:D.281 GOL.10: 8 residues within 4Å: Chain A: W.316, G.317, G.318, I.362, N.363, K.364, N.365, N.366 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.316, A:N.363, A:N.365, A:N.366, A:N.366, A:N.366 Water bridges: A:K.364, A:N.365

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.5: 5 residues within 4Å: Chain A: R.182, M.183, E.184, Q.185, K.195 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.184, A:Q.185 Salt bridges: A:K.195

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

EDO.6: 9 residues within 4Å: Chain A: R.225, R.277, R.278, L.284, P.285, V.286, R.287, T.333, E.335 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.277, A:R.277 EDO.7: 10 residues within 4Å: Chain A: L.189, R.193, M.291, G.293, G.294, F.296, Y.309, E.319, N.320, I.323 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.193, A:Y.309, A:E.319, A:E.319, A:N.320 EDO.8: 4 residues within 4Å: Chain A: E.159, R.160, D.161, F.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.161, A:D.161 EDO.12: 8 residues within 4Å: Chain A: T.255, W.267, Y.268, P.269 Chain B: P.6, V.7, P.8, T.9 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.6, A:W.267 EDO.13: 4 residues within 4Å: Chain B: T.13, S.14, A.15 Ligands: A2G.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.15

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

MN.9: 5 residues within 4Å: Chain A: D.209, H.211, H.344, R.347 Ligands: UDP.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.209, A:H.211, A:H.344, H2O.2 MN.17: 6 residues within 4Å: Chain C: D.209, H.211, H.344, V.345, R.347 Ligands: UDP.14 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.211, C:H.344

3 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Post Translational Modification)(Non-covalent)

A2G.11: 14 residues within 4Å: Chain A: D.484, S.486, L.495, H.498, L.500, K.501, G.502, N.503, Q.504 Chain B: T.13, S.14, A.15, P.16 Ligands: EDO.13 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.500 Hydrogen bonds: A:D.484, A:H.498, A:N.503, A:N.503, A:Q.504, B:T.13 A2G.18: 12 residues within 4Å: Chain C: D.484, S.486, L.495, H.498, L.500, K.501, N.503, Q.504 Chain D: T.13, S.14, A.15, P.16 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.484, C:H.498, C:N.503, C:N.503, C:N.503 A2G.19: 14 residues within 4Å: Chain A: P.386, D.444, M.446, A.447, H.460, M.462, G.463, G.464, N.465, Q.466 Chain E: T.10, S.11, T.12, T.13 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:N.465 Hydrogen bonds: A:D.444, A:M.446, A:H.460, A:N.465, E:T.13

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

NAG.15: 6 residues within 4Å: Chain C: Y.428, F.429, S.430, L.431, N.552 Ligands: NAG.16 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.428, C:F.429 NAG.16: 5 residues within 4Å: Chain C: E.376, R.426, H.427, Y.428 Ligands: NAG.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.427

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Collette, A.M. et al., An unusual dual sugar-binding lectin domain controls the substrate specificity of a mucin-type O-glycosyltransferase. Sci Adv (2024)

Release Date

2024-03-13

Peptides

Polypeptide N-acetylgalactosaminyltransferase 1 soluble form: AC
Mucin-5AC: BDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

B
D

D
F

E
H

Polypeptide N-acetylgalactosaminyltransferase 1 soluble form

Mucin-5AC

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