SMTL ID : 8ywr.1

Crystal structure of the Fab fragment of the anti-IL-6 antibody 68F2 in complex with a domain-swapped IL-6 dimer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.93 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

SO4.1: 5 residues within 4Å: Chain C: T.108, L.110, Y.144, K.170, Y.176 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.144 Salt bridges: C:K.170 SO4.2: 6 residues within 4Å: Chain B: G.44, K.45 Chain C: D.87, Y.89, R.103, G.104 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Y.89, B:K.45 SO4.3: 5 residues within 4Å: Chain F: T.108, L.110, Y.144, K.170, Y.176 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.176 Salt bridges: F:K.170 SO4.4: 6 residues within 4Å: Chain E: G.44, K.45 Chain F: D.87, Y.89, R.103, G.104 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Water bridges: F:D.87 Hydrogen bonds: E:K.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yudenko, A. et al., Structural basis of signaling complex inhibition by IL-6 domain-swapped dimers. Structure (2025)

Release Date

2024-11-06

Peptides

Interleukin-6: AD
Heavy chain of the Fab fragment of anti-IL-6 antibody 68F2: BE
Light chain of the Fab fragment of anti-IL-6 antibody 68F2: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

B
H

E
H

C
L

F
L

Interleukin-6

Heavy chain of the Fab fragment of anti-IL-6 antibody 68F2

Light chain of the Fab fragment of anti-IL-6 antibody 68F2

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