SMTL ID : 4c16.2 (1 other biounit)

E-selectin lectin, EGF-like and two SCR domains complexed with glycomimetic antagonist

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: L.176, Y.181, N.182 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.176 Hydrogen bonds: A:N.182 Water bridges: A:P.146, A:Y.181 NAG.2: 2 residues within 4Å: Chain A: N.139, Y.140 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.151 NAG.3: 4 residues within 4Å: Chain A: S.149, Q.155, I.156, N.158 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.155 Hydrogen bonds: A:Q.155, A:I.156, A:N.158 NAG.4: 3 residues within 4Å: Chain A: L.176, G.177, N.178 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.178, A:N.178, A:N.178 NAG.5: 2 residues within 4Å: Chain A: N.4, R.22 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.4, A:Y.18, A:Y.18 NAG.6: 1 residues within 4Å: Chain A: N.124 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain A: Y.193, W.243, N.244 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.244

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 6 residues within 4Å: Chain A: E.80, N.82, E.88, N.105, D.106 Ligands: FUC.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.80, A:E.88, A:D.106, A:D.106

1 x 4WC: (S)-CYCLOHEXYL LACTIC ACID(Non-covalent)

4WC.9: 3 residues within 4Å: Chain A: Y.48, R.97 Ligands: GAL.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.44, A:Y.48 Salt bridges: A:R.97

1 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.10: 9 residues within 4Å: Chain A: Y.48, E.92, Y.94, R.97, N.105, E.107 Ligands: 4WC.9, Q6Z.11, FUC.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.92, A:Y.94, A:R.97, A:R.97

1 x Q6Z: (1R,2R,3S)-3-methylcyclohexane-1,2-diol(Non-covalent)

Q6Z.11: 3 residues within 4Å: Chain A: Q.85 Ligands: GAL.10, FUC.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.85 Hydrogen bonds: A:Q.85

1 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.12: 11 residues within 4Å: Chain A: E.80, N.82, R.84, Q.85, E.88, N.105, D.106, E.107 Ligands: CA.8, GAL.10, Q6Z.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.82, A:Q.85, A:N.105, A:N.105, A:E.107 Water bridges: A:E.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Preston, R.C. et al., E-Selectin Ligand Complexes Adopt an Extended High-Affinity Conformation. J.Mol.Cell.Biol. (2016)

Release Date

2014-08-20

Peptides

E-SELECTIN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

E-SELECTIN

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