6PJV: Human Sonic Hedgehog

Structure of Human Sonic Hedgehog in complex with Zinc and Magnesium. Determined by X-ray diffraction at 1.43 Å resolution. Released 13 Nov 2019.

Method: X-ray diffraction
Resolution: 1.43 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,536
Mol. weight: 19.63 kDa
Ligands: MG, ZN
Released: 13 Nov 2019

Explore 6PJV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PJV contains 7 α-helices and 8 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	40-43	4
β-strand	47-48	2	1
α-helix	71-74	4
β-strand	77-78	2	2
β-strand	84-86	3	1
α-helix	94-96	3
β-strand	97-98	2	2
α-helix	100-116	17
β-strand	122-126	5	1
α-helix	139-141	3
β-strand	145-150	6	1
α-helix	155-157	3
α-helix	158-167	10
β-strand	172-177	6	1
β-strand	180-184	5	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sonic hedgehog protein	A	protein	169	Homo sapiens	Q15465 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6PJV_1 Sonic hedgehog protein (chains A)
GFGKRRHPKKLTPLAYKQFIPNVAEKTLGASGRYEGKISRNSERFKELTPNYNPDIIFKD
EENTGADRLMTQRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDI
TTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENSVAAKSGG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	1

Water and common crystallization additives (DMS, GOL, CL) are not listed.

Primary citation

Structure of Sonic Hedgehog protein in complex with zinc(II) and magnesium(II) reveals ion-coordination plasticity relevant to peptide drug design. Bonn-Breach, R., Gu, Y., Jenkins, J. et al. Acta Crystallogr D Struct Biol (2019) 75:969-979. DOI 10.1107/S2059798319012890 · PubMed

Other PDB entries of the same protein (UniProt Q15465 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8Z3A 1.75 Å, Crystal structure of Sonic hedgehog in complex with antibody 5E1 without metals
8Z39 1.8 Å, Crystal structure of Sonic hedgehog in complex with antibody 5E1 mutant L-T56A with metals
3MXW 1.83 Å, Crystal structure Sonic hedgehog bound to the 5E1 fab fragment
3M1N 1.85 Å, Crystal structure of Human Sonic Hedgehog N-terminal domain
8Z2V 1.89 Å, Crystal structure of Sonic hedgehog in complex with antibody 5E1 mutant H-R102A with…
8YYZ 1.9 Å, Crystal structure of Sonic hedgehog in complex with antibody 5E1 mutant H-R102A in the…
7URF 2.8 Å, Human HHAT H379C in complex with SHH N-terminal peptide
3HO5 3.01 Å, Crystal structure of Hedgehog-interacting protein (HHIP) and Sonic hedgehog (SHH) complex
7MHZ 3.2 Å, Human Hedgehog acyltransferase (HHAT) in complex with a palmitoylated Hedgehog peptide…
6RMG 3.4 Å, Structure of PTCH1 bound to a modified Hedgehog ligand ShhN-C24II
6E1H 3.5 Å, Structure of 2:1 human Ptch1-Shh-N complex
6RVD 3.5 Å, Revised cryo-EM structure of the human 2:1 Ptch1-Shh complex

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