5L7I: Human Smoothened

Structure of human Smoothened in complex with Vismodegib. Determined by X-ray diffraction at 3.3 Å resolution. Released 20 Jul 2016.

Method: X-ray diffraction
Resolution: 3.3 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 2
Atoms: 9,107
Mol. weight: 143.37 kDa
Ligands: NAG, VIS, MPG
Released: 20 Jul 2016

Explore 5L7I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5L7I contains 63 α-helices and 38 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: 32 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	58-61	4
β-strand	65-67	3	1
β-strand	71-72	2	1
α-helix	73	1
β-strand	77	1	2
β-strand	82	1	2
β-strand	87-88	2	1
α-helix	99-109	11
α-helix	110-112	3
β-strand	114	1	3
α-helix	116-130	15
β-strand	134	1	1
β-strand	138-140	3	1
α-helix	141-143	3
α-helix	144-151	8
α-helix	155-160	6
α-helix	165-167	3
β-strand	192	1	3
β-strand	197-199	3	4
α-helix	203-205	3
β-strand	206	1	4
β-strand	213-215	3	4
β-strand	216	1	5
α-helix	224-254	31
α-helix	256-259	4
α-helix	264-282	19
α-helix	283-285	3
α-helix	290-293	4
β-strand	295	1	6
β-strand	300	1	5
β-strand	301	1	6
α-helix	302	1
β-strand	305	1	7
α-helix	313-341	29
α-helix	354-356	3
α-helix	357-378	22
β-strand	381-384	4	7
β-strand	389-392	4	7
α-helix	397-400	4
α-helix	401-405	5
α-helix	406-1034	47
α-helix	1038-1056	19
α-helix	1075-1096	22
α-helix	1100-1112	13
α-helix	1113-1117	5
α-helix	1118-1128	11
α-helix	1131-449	5
α-helix	450-491	42
α-helix	515-533	19
α-helix	534-536	3
α-helix	540-550	11

Chain B: 31 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	59-61	3
β-strand	65-67	3	8
β-strand	71-72	2	8
α-helix	73	1
β-strand	77	1	9
β-strand	82	1	9
β-strand	87-88	2	8
α-helix	99-109	11
α-helix	110-112	3
β-strand	114	1	10
α-helix	116-130	15
β-strand	134	1	8
β-strand	138-140	3	8
α-helix	141-143	3
α-helix	144-151	8
α-helix	155-160	6
α-helix	165-167	3
β-strand	192	1	10
β-strand	197-199	3	11
α-helix	203-205	3
β-strand	206-207	2	11
β-strand	210-215	6	11
β-strand	216	1	12
α-helix	224-254	31
α-helix	256-259	4
α-helix	264-282	19
α-helix	283-285	3
α-helix	290-293	4
β-strand	295	1	13
β-strand	300	1	12
β-strand	301	1	13
α-helix	302	1
β-strand	305	1	14
α-helix	313-341	29
α-helix	342-344	3
α-helix	357-378	22
β-strand	381-384	4	14
β-strand	389-392	4	14
α-helix	397-400	4
α-helix	401-405	5
α-helix	406-1033	46
α-helix	1038-1056	19
α-helix	1076-1096	21
α-helix	1100-1112	13
α-helix	1113-1117	5
α-helix	1118-1129	12
α-helix	448-491	44
α-helix	515-533	19
α-helix	534-536	3
α-helix	540-551	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Smoothened homolog,Soluble cytochrome b562,Smoothened homolog	A, B	protein	638	Homo sapiens, Escherichia coli	P0ABE7 (AlphaFold model), Q99835 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5L7I_1 Smoothened homolog,Soluble cytochrome b562,Smoothened homolog (chains A, B)
SSGNATGPGPRSAGGSARRSAAVTGPPPPLSHCGRAAPCEPLRYNVCLGSVLPYGATSTL
LAGDSDSQEEAHGKLVLWSGLRNAPRCWAVIQPLLCAVYMPKCENDRVELPSRTLCQATR
GPCAIVERERGWPDFLRCTPDRFPEGCTNEVQNIKFNSSGQCEVPLVRTDNPKSWYEDVE
GCGIQCQNPLFTEAEHQDMHSYIAAFGAVTGLCTLFTLATFVADWRNSNRYPAVILFYVN
ACFFVGSIGWLAQFMDGARREIVCRADGTMRLGEPTSNETLSCVIIFVIVYYALMAGFVW
FVVLTYAWHTSFKALGTTYQPLSGKTSYFHLLTWSLPFVLTVAILAVAQVDGDSVSGICF
VGYKNYRYRAGFVLAPIGLVLIVGGYFLIRGVMTLFSARRQLADLEDNWETLNDNLKVIE
KADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKL
ANEGKVKEAQAAAEQLKTTRNAYIQKYLERARSTLSKINETMLRLGIFGFLAFGFVLITF
SCHFYDFFNQAEWERSFRDYVLCQANVTIGLPTKQPIPDCEIKNRPSLLVEKINLFAMFG
TGIAMSTWVWTKATLLIWRRTWCRLTGQGTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
VIS	2-chloranyl-~{N}-(4-chloranyl-3-pyridin-2-yl-phenyl)-4-methylsulfonyl-benzamide	C19 H14 Cl2 N2 O3 S	2
MPG	[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate	C21 H40 O4	2

Water and common crystallization additives (NA) are not listed.

Primary citation

Structural basis of Smoothened regulation by its extracellular domains. Byrne, E.F., Sircar, R., Miller, P.S. et al. Nature (2016) 535:517-522. DOI 10.1038/nature18934 · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

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