SMTL ID : 3mxw.1

Crystal structure Sonic hedgehog bound to the 5E1 fab fragment

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.112, D.119, E.148, H.154 Ligands: SO4.5 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.4

2 x CA: CALCIUM ION(Non-covalent)

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

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

SO4.4: 2 residues within 4Å: Chain A: R.73, K.77 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.73 Salt bridges: A:R.73, A:K.77 SO4.5: 7 residues within 4Å: Chain A: H.106, S.107, S.110, H.112, E.148, H.154 Ligands: ZN.1 12 PLIP interactions: 9 interactions with chain A, 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: A:S.107, A:S.110, A:E.148 Water bridges: A:H.106, A:H.106, A:S.110, A:L.111, C:R.102, B:N.53, B:N.53 Salt bridges: A:H.106, A:H.154 SO4.6: 4 residues within 4Å: Chain B: Q.37, K.39, Q.42, K.45 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.37, B:Q.42 Water bridges: B:Q.37, B:K.39 Salt bridges: B:K.39, B:K.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maun, H.R. et al., Hedgehog pathway antagonist 5E1 binds hedgehog at the pseudo-active site. J.Biol.Chem. (2010)

Release Date

2010-05-26

Peptides

Sonic hedgehog protein: A
5E1 light chain: B
5E1 heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
L

C
H

Sonic hedgehog protein

5E1 light chain

5E1 heavy chain

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