SMTL ID : 8yyz.1

Crystal structure of Sonic hedgehog in complex with antibody 5E1 mutant H-R102A in the absence of metals

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: S.123, D.124 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain B: T.87, S.88 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain C: S.114, V.115, K.207 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain C: S.114, N.137 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain C: T.197 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: R.127 Chain B: W.47, V.50, R.52, N.59, D.104 Chain C: S.94, P.96 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.127, B:R.52, B:R.52, B:D.104

2 x IOD: IODIDE ION(Non-functional Binders)

IOD.3: 2 residues within 4Å: Chain B: V.175 Chain C: Q.160 Ligand excluded by PLIP IOD.5: 3 residues within 4Å: Chain C: S.28, S.30, Y.67 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaneda, I. et al., Biophysical insights to improve affinity of antibodies to fluctuated epitope of antigen: A case of anti-Shh antibody 5E1 against Shh antigen. To Be Published

Release Date

2025-04-09

Peptides

Sonic hedgehog protein N-product: A
Heavy chain antibody 5E1 mutated: B
Light chain antibody 5E1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Sonic hedgehog protein N-product

Heavy chain antibody 5E1 mutated

Light chain antibody 5E1

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