SMTL ID : 6pjv.1

Structure of Human Sonic Hedgehog in complex with Zinc and Magnesium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

monomer

Ligands

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 6 residues within 4Å: Chain A: P.50, Y.52, G.65, A.66, R.68, L.69 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.40 DMS.2: 6 residues within 4Å: Chain A: E.25, K.26, W.144, Y.146, E.148, H.154 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.26 Water bridges: A:E.25 Salt bridges: A:E.25, A:E.148 pi-Cation interactions: A:H.154 DMS.3: 5 residues within 4Å: Chain A: F.19, A.24, E.25, W.144, Y.146 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: Q.88, W.89, S.128, K.129, M.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.88, A:W.89 Water bridges: A:M.132

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: E.62, D.67, E.98 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.62, A:E.98, H2O.1, H2O.1, H2O.1, H2O.4 MG.7: 6 residues within 4Å: Chain A: H.112, D.119, E.148, H.152, H.154 Ligands: ZN.6 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.112, A:D.119, A:E.148, A:H.154, H2O.1, H2O.1

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 6 residues within 4Å: Chain A: H.112, D.119, E.148, H.152, H.154 Ligands: MG.7 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.112, A:D.119, A:E.148, A:H.154, H2O.1, H2O.1

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

CL.8: 3 residues within 4Å: Chain A: N.53, K.75, N.79 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: I.57, K.59, R.95, R.125 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bonn-Breach, R. et al., Structure of Sonic Hedgehog protein in complex with zinc(II) and magnesium(II) reveals ion-coordination plasticity relevant to peptide drug design. Acta Crystallogr D Struct Biol (2019)

Release Date

2019-11-13

Peptides

Sonic hedgehog protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sonic hedgehog protein

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