SMTL ID : 8z2v.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

CL.1: 6 residues within 4Å: Chain A: H.106, S.107, S.110, H.112, H.154 Ligands: ZN.2 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.112, D.119, E.148, H.154 Ligands: CL.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.112, A:D.119, A:D.119, A:H.154, H2O.2

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: E.61, E.62, D.67, T.97, E.98 Ligands: CA.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.62, A:D.67, A:D.67, A:T.97, A:E.98 CA.4: 5 residues within 4Å: Chain A: E.62, E.98, D.101, D.103 Ligands: CA.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.62, A:D.101, A:D.103, H2O.1, H2O.3

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: R.127 Chain B: W.47, V.50, R.52, D.104 Chain C: S.94, P.96 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:R.127, A:R.127, B:R.52, B:R.52, C:S.94, C:S.94

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

2025-04-16

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Sonic hedgehog protein N-product

Heavy chain of antibody 5E1

Light chain of antibody 5E1

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