6RTY: Patched ectodomain

Crystal structure of the Patched ectodomain in complex with nanobody NB64. Determined by X-ray diffraction at 2.1 Å resolution. Released 2 Oct 2019.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Homo sapiens, Lama glama
Chains: 2
Atoms: 3,270
Mol. weight: 48.85 kDa
Ligands: NAG
Released: 2 Oct 2019

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

Secondary structure: helices and β-sheets

6RTY contains 18 α-helices and 29 β-strands across 2 chains. 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: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	154-162	9	1
α-helix	172-186	15
β-strand	190-192	3	2
β-strand	195-197	3	2
α-helix	199-202	4
β-strand	203	1	1
β-strand	205-210	6	3
α-helix	214-223	10
α-helix	225-226	2
β-strand	228-229	2	1
α-helix	231-234	4
α-helix	236-241	6
β-strand	246	1	4
α-helix	252-253	2
β-strand	254	1	4
α-helix	261-270	10
α-helix	276-285	10
α-helix	295-296	2
α-helix	316-317	2
α-helix	319-323	5
β-strand	327-328	2	5
β-strand	336-337	2	5
α-helix	339-342	4
β-strand	343-344	2	1
β-strand	347-348	2	6
β-strand	354-356	3	6
β-strand	359-366	8	1
α-helix	367-368	2
α-helix	369-376	8
α-helix	380-382	3
α-helix	389-409	21
β-strand	417-422	6	1

Chain B: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	11-12	2	8
β-strand	18-24	7	7
β-strand	33-39	7	3
β-strand	46-52	7	3
β-strand	57-59	3	3
β-strand	64	1	7
β-strand	67-69	3	7
β-strand	72	1	7
β-strand	77-82	6	7
α-helix	87-89	3
β-strand	91-101	11	3
β-strand	103-110	8	3
β-strand	114-116	3	3
β-strand	117-118	2	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein patched homolog 1	A	protein	297	Homo sapiens	Q13635 (AlphaFold model)
Llama-derived nanobody NB64	B	protein	130	Lama glama

Sequence of entity 1 (A), FASTA

>6RTY_1 Protein patched homolog 1 (chains A)
ETGELNYTRQKIGEEAMFNPQLMIQTPKEEGANVLTTEALLQHLDSALQASRVHVYMYNR
QWKLEHLCYKSGELITETGYMDQIIEYLYPCLIITPLDCFWEGAKLQSGTAYLLGKPPLR
WTNFDPLEFLEELKKINYQVDSWEEMLNKAEVGHGYMDRPCLNPADPDCPATAPNKNSTK
PLDMALVLNGGCHGLSRKYMHWQEELIVGGTVKNSTGKLVSAHALQTMFQLMTPKQMYEH
FKGYEYVSHINWNEDKAAAILEAWQRTYVEVVHQSVAQNSTQKVLSFTGTKHHHHHH

Sequence of entity 2 (B), FASTA

>6RTY_2 Llama-derived nanobody NB64 (chains B)
QVQLQESGGGLVQPGGSLRLSCAASGSGNSINVMGWYRQAPGKPRELVAEITSSGTTNYA
DSVKGRFSISRDNAKNTVPLQMNSLKPEDTAIYYCSAVLVRFGGLRRSYWGQGTQVTVSS
HHHHHHEPEA

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

The morphogen Sonic hedgehog inhibits its receptor Patched by a pincer grasp mechanism. Rudolf, A.F., Kinnebrew, M., Kowatsch, C. et al. Nat Chem Biol (2019) 15:975-982. DOI 10.1038/s41589-019-0370-y · PubMed

Other PDB entries of the same protein (UniProt Q13635 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6RTW 1.9 Å, Crystal structure of the Patched-1 (PTCH1) ectodomain in complex with nanobody NB64 and…
6RTX 1.95 Å, Crystal structure of the Patched-1 (PTCH1) ectodomain 1
6RVC 2.2 Å, Crystal structure of Patched-1 ectodomain 2 (PTCH1-ECD2) in complex with nanobody 75
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
6OEU 3.5 Å, Structure of human Patched1
6RVD 3.5 Å, Revised cryo-EM structure of the human 2:1 Ptch1-Shh complex
6DMY 3.6 Å, Cryo-EM structure of human Ptch1 and ShhN complex
6N7H 3.6 Å, Cryo-EM structure of the 2:1 hPtch1-Shhp complex
9MS8 3.73 Å, PTCH1 in complex with Fab6H3
6OEV 3.8 Å, Structure of human Patched1 in complex with native Sonic Hedgehog
6DMB 3.9 Å, Cryo-EM structure of human Ptch1

Browse structure collections

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