SMTL ID : 5vc1.1

Crystal structure of L-selectin lectin/EGF domains

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

monomer

Ligands

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

NAG-NAG-MAN-BMA-BMA.1: 1 residues within 4Å: Chain A: N.66 No protein-ligand interaction detected (PLIP)

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 6 residues within 4Å: Chain A: R.16, R.20, D.25, I.56, V.63, G.64 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.16, A:R.16, A:R.20, A:D.25, A:G.64

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

PEG.3: 5 residues within 4Å: Chain A: L.69, T.70, E.71, E.74, W.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.76

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: N.83, N.86, D.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.86 Water bridges: A:N.86

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: E.80, N.82, E.88, N.105, D.106 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.80, A:E.88, A:D.106, A:D.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wedepohl, S. et al., Reducing Macro- and Microheterogeneity of N-Glycans Enables the Crystal Structure of the Lectin and EGF-Like Domains of Human L-Selectin To Be Solved at 1.9 angstrom Resolution. Chembiochem (2017)

Release Date

2017-06-14

Peptides

L-selectin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L-selectin