SMTL ID : 6usc.1 (1 other biounit)

Structure of Human Intelectin-1 in complex with KO

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-trimer

Ligands

9 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: N.226, E.228, E.240 Ligands: KO2.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.228, A:E.240, H2O.4, H2O.4 CA.2: 4 residues within 4Å: Chain A: H.52, G.63, D.99, D.248 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.52, A:D.99, A:D.248, H2O.2, H2O.4 CA.3: 4 residues within 4Å: Chain A: E.53, D.55, G.58, D.64 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.55, A:G.58, A:D.64, H2O.3, H2O.4 CA.6: 4 residues within 4Å: Chain B: N.226, E.228, E.240 Ligands: KO2.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.228, B:E.240, H2O.10, H2O.10 CA.7: 4 residues within 4Å: Chain B: H.52, G.63, D.99, D.248 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.52, B:D.99, B:D.248, H2O.8, H2O.10 CA.8: 4 residues within 4Å: Chain B: E.53, D.55, G.58, D.64 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.55, B:G.58, B:D.64, H2O.9, H2O.10 CA.11: 4 residues within 4Å: Chain C: N.226, E.228, E.240 Ligands: KO2.14 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.228, C:E.240, H2O.16, H2O.16 CA.12: 4 residues within 4Å: Chain C: H.52, G.63, D.99, D.248 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.52, C:D.99, C:D.248, H2O.14, H2O.16 CA.13: 4 residues within 4Å: Chain C: E.53, D.55, G.58, D.64 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.55, C:G.58, C:D.64, H2O.15, H2O.16

3 x KO2: prop-2-en-1-yl D-glycero-alpha-D-talo-oct-2-ulopyranosidonic acid(Non-covalent)

KO2.4: 8 residues within 4Å: Chain A: Y.192, N.226, E.228, H.229, E.240, W.254, Y.263 Ligands: CA.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.192, A:Y.263 Hydrogen bonds: A:E.228, A:H.229, A:E.240, A:E.240, A:W.254 KO2.9: 8 residues within 4Å: Chain B: Y.192, N.226, E.228, H.229, E.240, W.254, Y.263 Ligands: CA.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.192, B:Y.263 Hydrogen bonds: B:E.228, B:H.229, B:E.240, B:E.240, B:W.254 KO2.14: 8 residues within 4Å: Chain C: Y.192, N.226, E.228, H.229, E.240, W.254, Y.263 Ligands: CA.11 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.192, C:Y.263 Hydrogen bonds: C:H.229, C:E.240, C:E.240, C:W.254

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 2 residues within 4Å: Chain A: Y.22, F.23 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: Y.22, F.23 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain C: Y.22, F.23 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

McMahon, C.M. et al., Stereoelectronic Effects Impact Glycan Recognition. J.Am.Chem.Soc. (2020)

Release Date

2020-01-22

Peptides

Intelectin-1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Intelectin-1

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