SMTL ID : 8fia.1

The structure of fly Teneurin self assembly

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.1: 6 residues within 4Å: Chain A: N.82, S.84, W.154, Q.392, T.425, D.426 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.426 Water bridges: A:T.425 NAG-NAG-BMA-MAN-MAN-MAN.16: 6 residues within 4Å: Chain B: N.82, S.84, W.154, Q.392, T.425, D.426 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.426 Water bridges: B:T.425

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 6 residues within 4Å: Chain A: N.436, T.438, R.439, E.461, S.462, W.481 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.461 NAG-NAG-FUC.17: 6 residues within 4Å: Chain B: N.436, T.438, R.439, E.461, S.462, W.481 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.461

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

NAG-NAG-BMA-MAN-MAN-FUC.3: 8 residues within 4Å: Chain A: Q.1037, S.1057, G.1058, D.1059, A.1314, F.1315, N.1316, Y.1333 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.1037, A:S.1057, A:G.1058 NAG-NAG-BMA-MAN-MAN-FUC.18: 8 residues within 4Å: Chain B: Q.1037, S.1057, G.1058, D.1059, A.1314, F.1315, N.1316, Y.1333 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.1037, B:S.1057, B:G.1058

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.4: 6 residues within 4Å: Chain A: T.1026, S.1028, V.1030, E.1038, N.1041, T.1043 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 6 residues within 4Å: Chain B: T.1026, S.1028, V.1030, E.1038, N.1041, T.1043 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.5: 6 residues within 4Å: Chain A: W.1484, D.1486, K.1488, N.1490, P.1590, H.1591 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 6 residues within 4Å: Chain B: W.1484, D.1486, K.1488, N.1490, P.1590, H.1591 No protein-ligand interaction detected (PLIP)

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

NAG.6: 7 residues within 4Å: Chain A: E.826, S.828, N.832, N.834, S.852, D.1133, A.1134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.828 NAG.7: 5 residues within 4Å: Chain A: M.1812, N.1814, H.1834, G.1835, P.1836 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.1836 Hydrogen bonds: A:N.1814 NAG.15: 3 residues within 4Å: Chain A: V.1753, N.1772, N.1773 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1772 NAG.21: 7 residues within 4Å: Chain B: E.826, S.828, N.832, N.834, S.852, D.1133, A.1134 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.828 NAG.22: 5 residues within 4Å: Chain B: M.1812, N.1814, H.1834, G.1835, P.1836 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.1836 Hydrogen bonds: B:N.1814 NAG.30: 3 residues within 4Å: Chain B: V.1753, N.1772, N.1773 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1772

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: D.161, R.264, K.307, W.320 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.264 GOL.9: 9 residues within 4Å: Chain A: G.91, R.92, W.123, I.160, D.161, L.162, R.264, L.271, E.273 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.92, A:R.264, A:R.264, A:E.273 Water bridges: A:D.161, A:D.161, A:E.273, A:E.273 GOL.12: 9 residues within 4Å: Chain A: A.407, P.408, D.409, F.413, R.422, L.448, G.453, T.471, N.472 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.409, A:R.422, A:R.422, A:G.453, A:T.471 Water bridges: A:R.85 GOL.13: 2 residues within 4Å: Chain A: K.506, D.507 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.506, A:D.507 GOL.14: 8 residues within 4Å: Chain A: I.372, L.373, T.374, F.685, A.687, H.689, Y.690, R.722 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.687, A:R.722, A:R.722 GOL.23: 4 residues within 4Å: Chain B: D.161, R.264, K.307, W.320 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.264 GOL.24: 9 residues within 4Å: Chain B: G.91, R.92, W.123, I.160, D.161, L.162, R.264, L.271, E.273 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.92, B:R.264, B:R.264, B:E.273 Water bridges: B:D.161, B:L.162, B:E.273, B:E.273 GOL.27: 9 residues within 4Å: Chain B: A.407, P.408, D.409, F.413, R.422, L.448, G.453, T.471, N.472 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.409, B:R.422, B:R.422, B:G.453, B:T.471 Water bridges: B:R.85 GOL.28: 4 residues within 4Å: Chain A: E.969, G.972 Chain B: K.506, D.507 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.506, B:D.507 GOL.29: 8 residues within 4Å: Chain B: I.372, L.373, T.374, F.685, A.687, H.689, Y.690, R.722 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.374, B:A.687, B:R.722, B:R.722

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 8 residues within 4Å: Chain A: D.620, R.664, V.886, K.887, G.888, I.905, Q.906, G.907 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.620, A:D.620, A:R.664, A:R.664, A:G.907 PEG.11: 5 residues within 4Å: Chain A: G.927, T.929, I.1699, V.1700, T.1703 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.1699, A:T.1703 PEG.25: 8 residues within 4Å: Chain B: D.620, R.664, V.886, K.887, G.888, I.905, Q.906, G.907 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.620, B:D.620, B:R.664, B:R.664, B:G.907 PEG.26: 5 residues within 4Å: Chain B: G.927, T.929, I.1699, V.1700, T.1703 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.1699

Links

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Citation

Li, J. et al., The structure of fly Teneurin-m reveals an asymmetric self-assembly that allows expansion into zippers. Embo Rep. (2023)

Release Date

2023-05-03

Peptides

Teneurin-m: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Teneurin-m