SMTL ID : 6eyk.1

E-selectin lectin, EGF-like and two SCR domains complexed with glycomimetic ligand NV355

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 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 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.176 Hydrogen bonds: A:N.182 NAG.2: 4 residues within 4Å: Chain A: N.139, Y.140, L.151, K.152 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.138 NAG.3: 5 residues within 4Å: Chain A: S.149, Q.155, I.156, N.158 Ligands: NAG.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.155 Hydrogen bonds: A:Q.155, A:I.156 NAG.4: 2 residues within 4Å: Chain A: N.178 Ligands: NAG.3 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain A: N.4, R.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.22, A:R.22 NAG.6: 1 residues within 4Å: Chain A: N.124 No protein-ligand interaction detected (PLIP) NAG.7: 4 residues within 4Å: Chain A: Y.193, V.218, W.243, N.244 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.218, A:W.243 Hydrogen bonds: A:N.244

1 x C5K: (2~{S})-3-cyclohexyl-2-[(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[(1~{R},2~{R},3~{S})-3-methyl-2-[(2~{R},3~{S},4~{R},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(trifluoromethyl)oxan-2-yl]oxy-cyclohexyl]oxy-3,5-bis(oxidanyl)oxan-4-yl]oxy-propanoic acid(Non-covalent)

C5K.8: 15 residues within 4Å: Chain A: Y.44, Y.48, E.80, N.82, R.84, Q.85, E.88, E.92, Y.94, R.97, E.98, N.105, D.106, E.107 Ligands: CA.9 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Q.85 Hydrogen bonds: A:Y.44, A:E.80, A:N.82, A:Q.85, A:E.92, A:Y.94, A:R.97, A:E.98, A:E.98, A:N.105, A:E.107 Salt bridges: A:R.84, A:R.97

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 6 residues within 4Å: Chain A: E.80, N.82, E.88, N.105, D.106 Ligands: C5K.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.80, A:E.88, A:D.106, A:D.106 CA.10: 1 residues within 4Å: Chain A: G.168 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.168, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Varga, N. et al., Strengthening an Intramolecular Non-Classical Hydrogen Bond to Get in Shape for Binding. Angew.Chem.Int.Ed.Engl. (2024)

Release Date

2018-11-21

Peptides

E-selectin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E-selectin

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