SMTL ID : 3i9g.1

Crystal structure of the LT1009 (SONEPCIZUMAB) antibody Fab fragment in complex with sphingosine-1-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-oligomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain B: D.30, D.31, D.32 Ligands: CA.2, S1P.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.30, B:D.31, B:D.32, H2O.140, H2O.143 CA.2: 5 residues within 4Å: Chain B: D.30, D.32, D.92 Ligands: CA.1, S1P.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.30, B:D.32, B:D.92, H2O.141, H2O.142

5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 2 residues within 4Å: Chain B: S.12, K.107 No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain B: Q.155 No protein-ligand interaction detected (PLIP)

1 x S1P: (2S,3R,4E)-2-AMINO-3-HYDROXYOCTADEC-4-EN-1-YL DIHYDROGEN PHOSPHATE(Non-covalent)

S1P.8: 20 residues within 4Å: Chain A: T.33, S.52, H.55, I.57, K.59, F.101, Y.102, G.103, S.104, W.107 Chain B: D.30, D.32, E.50, S.91, D.92, N.93, L.94, F.96 Ligands: CA.1, CA.2 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:T.33, A:K.59, A:F.101, A:Y.102, A:W.107, B:L.94, B:F.96 Hydrogen bonds: A:G.103, A:G.103, B:D.32, B:D.32 Water bridges: B:E.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wojciak, J.M. et al., The crystal structure of sphingosine-1-phosphate in complex with a Fab fragment reveals metal bridging of an antibody and its antigen. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-09-29

Peptides

Sonepcizumab antibody Fab fragment, heavy chain: A
Sonepcizumab antibody Fab fragment, light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

Sonepcizumab antibody Fab fragment, heavy chain

Sonepcizumab antibody Fab fragment, light chain