SMTL ID : 5fb8.1

Structure of Interleukin-16 bound to the 14.1 antibody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

hetero-1-1-1-mer

Ligands

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 1 residues within 4Å: Chain A: R.215 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.191 Salt bridges: A:R.215 SO4.2: 4 residues within 4Å: Chain A: Q.41, K.43, Q.46, K.49 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.46 Water bridges: A:Q.41, A:K.43, A:K.43, A:K.43 Salt bridges: A:K.43, A:K.49 SO4.7: 6 residues within 4Å: Chain B: V.2, Y.27, Y.32, R.98 Chain C: E.28 Ligands: TRS.11 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:E.28, C:E.28 Salt bridges: B:R.98

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: Q.42, K.43, P.44, G.45, Q.46 Chain B: Y.95 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:Q.39 Hydrogen bonds: A:Q.42, A:G.45, A:Q.46 EDO.4: 4 residues within 4Å: Chain A: L.15, E.84, R.112, D.174 No protein-ligand interaction detected (PLIP) EDO.5: 5 residues within 4Å: Chain A: S.125, D.126, E.127 Chain B: P.131, K.222 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.217, A:D.126, A:E.127, A:E.127 EDO.6: 6 residues within 4Å: Chain A: P.123, Y.190, N.214, R.215, G.216, E.217 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.190, A:G.216, A:E.217 EDO.8: 3 residues within 4Å: Chain B: N.52, Y.101 Ligands: EDO.9 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Water bridges: C:W.80, C:K.84 Hydrogen bonds: B:N.52 EDO.9: 7 residues within 4Å: Chain B: T.33, L.50, N.52, G.57, T.58, N.59 Ligands: EDO.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.59 Water bridges: B:T.58, B:T.58 EDO.10: 3 residues within 4Å: Chain B: T.30, Y.54, K.74 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.30, B:K.74

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.11: 10 residues within 4Å: Chain B: Y.27, S.28, Y.32 Chain C: E.28, G.29, S.33, L.34, K.38, R.76 Ligands: SO4.7 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.29, C:L.34, C:K.38, C:K.38, C:R.76, B:S.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hall, G. et al., Structure of a Potential Therapeutic Antibody Bound to Interleukin-16 (IL-16): MECHANISTIC INSIGHTS AND NEW THERAPEUTIC OPPORTUNITIES. J.Biol.Chem. (2016)

Release Date

2016-06-08

Peptides

Anti-IL-16 antibody 14.1 Fab domain Kappa Chain: A
Anti-IL-16 antibody 14.1 Fab domain Heavy Chain: B
Pro-interleukin-16: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Anti-IL-16 antibody 14.1 Fab domain Kappa Chain

Anti-IL-16 antibody 14.1 Fab domain Heavy Chain

Pro-interleukin-16