SMTL ID : 4hwb.1

Crystal structure of ectodomain 3 of the IL-13 receptor alpha 1 in complex with a human neutralizing monoclonal antibody fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.91, K.93 Chain C: S.30 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Water bridges: A:R.91, C:S.31 Salt bridges: A:R.91, A:K.93 Hydrogen bonds: C:S.30 SO4.2: 1 residues within 4Å: Chain A: R.89 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.89 SO4.6: 2 residues within 4Å: Chain B: K.20, Q.83 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.83 Salt bridges: B:K.20 SO4.7: 3 residues within 4Å: Chain B: K.14, S.121, T.122 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.122, B:T.122, B:T.122 Salt bridges: B:K.14 SO4.8: 3 residues within 4Å: Chain B: K.13, E.17, S.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.18 Salt bridges: B:K.13 SO4.9: 3 residues within 4Å: Chain B: N.205, K.207, K.212 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.205, B:N.205 Water bridges: B:K.212 Salt bridges: B:K.207, B:K.212 SO4.10: 4 residues within 4Å: Chain B: V.3, Y.28, Y.33, R.99 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.108, B:Y.108 Salt bridges: B:R.99 SO4.13: 4 residues within 4Å: Chain C: K.40, Q.43, R.46 Ligands: SO4.16 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.43 Salt bridges: C:K.40, C:R.46 SO4.14: 1 residues within 4Å: Chain C: R.208 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.208 SO4.15: 3 residues within 4Å: Chain C: P.8, G.9, T.10 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.9, C:T.10 Water bridges: C:T.10 SO4.16: 6 residues within 4Å: Chain C: K.40, R.46, P.60, R.62, E.82 Ligands: SO4.13 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:K.40, C:R.46, C:R.62 SO4.17: 2 residues within 4Å: Chain C: R.55, S.64 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.55 SO4.18: 3 residues within 4Å: Chain C: P.60, D.61, R.62 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.62 Salt bridges: C:R.62

5 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.3: 10 residues within 4Å: Chain A: F.31, R.34, E.100, W.105, S.106, N.107, W.108, S.109 Chain B: Y.58 Ligands: NHE.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.31 Hydrogen bonds: A:N.107, A:N.107, A:N.107 Salt bridges: A:R.34 NHE.4: 10 residues within 4Å: Chain A: D.7, P.9, W.25, N.27, P.28, Q.29, N.30, F.31 Chain B: D.56 Ligands: NHE.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.9, A:W.25, A:N.27 Hydrogen bonds: A:N.27, A:Q.29, A:N.30, A:N.30, A:F.31 NHE.5: 7 residues within 4Å: Chain A: L.36, F.37, Y.38, Q.56, E.57, A.58, K.59 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.36, A:A.58 Hydrogen bonds: A:A.58 NHE.11: 7 residues within 4Å: Chain A: L.97, Y.99, E.100, D.101 Chain B: R.60, Y.61 Chain C: E.93 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.97 Hydrogen bonds: A:D.101, B:R.60 Salt bridges: B:R.60 NHE.12: 7 residues within 4Å: Chain A: E.100, N.107 Chain B: Y.58, T.59, R.60, Y.61, Q.66 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.58 Hydrogen bonds: B:Y.61, B:Y.61 Salt bridges: B:R.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Redpath, N.T. et al., Crystal structure of ectodomain 3 of the IL-13 receptor alpha 1 in complex with a human neutralizing monoclonal antibody fragment. Biochem.J. (2013)

Release Date

2013-02-27

Peptides

Interleukin-13 receptor subunit alpha-1: A
Fab heavy chain: B
Fab light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Interleukin-13 receptor subunit alpha-1

Fab heavy chain

Fab light chain

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