SMTL ID : 9bfs.1

Cryo-EM structure of Sevenless extracellular domain (dimer, pH 6.6)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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.1: 4 residues within 4Å: Chain A: E.1213, R.1229, N.1231, A.1257 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.3: 4 residues within 4Å: Chain B: E.1213, R.1229, N.1231, A.1257 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.2: 9 residues within 4Å: Chain A: N.844, S.846, V.847, H.864, G.868, C.869, P.870, P.905, W.906 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.870 Hydrogen bonds: A:G.868 NAG-NAG.4: 9 residues within 4Å: Chain B: N.844, S.846, V.847, H.864, G.868, C.869, P.870, P.905, W.906 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.870 Hydrogen bonds: B:G.868

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

NAG.5: 7 residues within 4Å: Chain A: A.1413, Q.1414, S.1415, N.1435, T.1437, D.1438, L.1442 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.1428 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: G.1104, N.1106 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.1517, W.1518 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain A: T.1185, Q.1188, N.1191, E.1240, H.1241 Ligand excluded by PLIP NAG.10: 7 residues within 4Å: Chain A: Q.1601, N.1603, P.1621, Q.1624, S.1647, G.1648, I.1649 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.1634 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: N.383, F.403, V.404, Q.405 Ligand excluded by PLIP NAG.13: 6 residues within 4Å: Chain B: A.1413, S.1415, N.1435, T.1437, D.1438, L.1442 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain B: N.1428 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: G.1104, N.1106 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.1517, W.1518 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain B: T.1185, Q.1188, N.1191, E.1240, H.1241 Ligand excluded by PLIP NAG.18: 6 residues within 4Å: Chain B: Q.1601, N.1603, Q.1624, S.1647, G.1648, I.1649 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.1634 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: N.383, F.403, V.404, Q.405 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cerutti, G. et al., Structures and pH-dependent dimerization of the sevenless receptor tyrosine kinase. Mol.Cell (2024)

Release Date

2025-01-29

Peptides

Protein sevenless: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein sevenless

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