5V57: Smoothened homolog,Flavodoxin,Smoothened homolog

3.0A SYN structure of the multi-domain human smoothened receptor in complex with TC114. Determined by X-ray diffraction at 3.0 Å resolution. Released 24 May 2017.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Homo sapiens, Desulfovibrio vulgaris
Chains: 2
Atoms: 10,101
Mol. weight: 146.65 kDa
Ligands: OLC, FMN, 836
Released: 24 May 2017

Explore 5V57 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V57 contains 59 α-helices and 54 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: 29 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	59-61	3
β-strand	65-67	3	1
β-strand	71-72	2	2
β-strand	77-78	2	3
β-strand	81-82	2	3
β-strand	87-88	2	2
α-helix	99-109	11
α-helix	110-113	4
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
β-strand	197-199	3	4
α-helix	203-205	3
β-strand	207	1	5
β-strand	210	1	5
β-strand	213-215	3	4
β-strand	216	1	6
α-helix	224-253	30
α-helix	256-259	4
α-helix	262-282	21
α-helix	283-285	3
α-helix	289-294	6
β-strand	295	1	7
β-strand	300	1	6
β-strand	301	1	7
β-strand	305	1	8
α-helix	313-343	31
α-helix	357-378	22
β-strand	381-383	3	8
β-strand	390-392	3	8
α-helix	397-400	4
α-helix	401-405	5
α-helix	406-431	26
β-strand	1003-1009	7	9
α-helix	1014-1028	15
β-strand	1032-1037	6	9
α-helix	1038-1040	3
β-strand	1052-1057	6	9
β-strand	1059-1060	2	10
β-strand	1066-1067	2	10
α-helix	1072-1076	5
α-helix	1078-1080	3
β-strand	1087-1094	8	9
α-helix	1103-1115	13
β-strand	1118-1119	2	9
β-strand	1124-1127	4	9
α-helix	1131-1133	3
α-helix	1134-1146	13
α-helix	447-491	45
α-helix	515-533	19
α-helix	534-536	3
α-helix	539-553	15

Chain B: 30 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	59-61	3
β-strand	65-67	3	11
β-strand	71-72	2	12
β-strand	77-78	2	13
β-strand	81-82	2	13
β-strand	87-88	2	12
α-helix	99-109	11
α-helix	110-113	4
β-strand	114	1	14
α-helix	116-130	15
β-strand	134	1	11
β-strand	138-140	3	11
α-helix	141-143	3
α-helix	144-151	8
α-helix	155-160	6
β-strand	192	1	14
β-strand	197-199	3	15
β-strand	207	1	16
β-strand	210	1	16
β-strand	213-215	3	15
β-strand	216	1	17
α-helix	224-254	31
α-helix	258-260	3
α-helix	262-282	21
α-helix	283-285	3
α-helix	289-294	6
β-strand	295	1	18
β-strand	300	1	17
β-strand	301	1	18
β-strand	305	1	19
α-helix	313-344	32
α-helix	345-347	3
α-helix	357-378	22
β-strand	381-383	3	19
β-strand	390-392	3	19
α-helix	397-400	4
α-helix	401-405	5
α-helix	406-426	21
α-helix	429-430	2
β-strand	1002-1009	8	20
α-helix	1014-1028	15
β-strand	1031-1037	7	20
α-helix	1038-1040	3
β-strand	1052-1057	6	20
β-strand	1059-1060	2	21
β-strand	1066-1067	2	21
α-helix	1072-1076	5
α-helix	1078-1080	3
β-strand	1087-1094	8	20
α-helix	1103-1115	13
β-strand	1118-1119	2	20
β-strand	1124-1127	4	20
α-helix	1130-1133	4
α-helix	1134-1146	13
α-helix	447-491	45
α-helix	515-533	19
α-helix	534-536	3
α-helix	539-553	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Smoothened homolog,Flavodoxin,Smoothened homolog	A, B	protein	648	Homo sapiens, Desulfovibrio vulgaris	P00323 (AlphaFold model), Q99835 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5V57_1 Smoothened homolog,Flavodoxin,Smoothened homolog (chains A, B)
PPPLSHCGRAAPCEPLRYNVCLGSVLPYGATSTLLAGDSDSQEEAHGKLVLWSGLRNAPR
CWAVIQPLLCAVYMPKCENDRVELPSRTLCQATRGPCAIVERERGWPDFLRCTPDRFPEG
CTNEVQNIKFNSSGQCEVPLVRTDNPKSWYEDVEGCGIQCQNPLFTEAEHQDMHSYIAAF
GAVTGLCTLFTLATFVADWRNSNRYPAVILFYVNACFFVGSIGWLAQFMDGARREIVCRA
DGTMRLGEPTSNETLSCVIIFVIVYYALMAGVVWFVVLTYAWHTSFKALGTTYQPLSGKT
SYFHLLTWSLPFVLTVAILAVAQVDGDSVSGICFVGYKNYRYRAGFVLAPIGLVLIVGGY
FLIRGVMTLFSIKSNHAKALIVYGSTTGNTEYTAETIARELADAGYEVDSRDAASVEAGG
LFEGFDLVLLGCSTWGDDSIELQDDFIPLFDSLEETGAQGRKVACFGCGDSSWEYFCGAV
DAIEEKLKNLGAEIVQDGLRIDGDPRAARDDIVGWAHDVRGAIKINETMLRLGIFGFLAF
GFVLITFSCHFYDFFNQAEWERSFRDYVLCQANVTIGLPTKQPIPDCEIKNRPSLLVEKI
NLFAMFGTGIAMSTWVWTKATLLIWRRTWCRLTGQSDDHHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	1
FMN	Flavin mononucleotide	C17 H21 N4 O9 P	2
836	N-methyl-N-[1-[4-(2-methylpyrazol-3-yl)phthalazin-1-yl]piperidin-4-yl]-4-nitro-…	C26 H24 F3 N7 O3	2

Primary citation

Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand. Zhang, X., Zhao, F., Wu, Y. et al. Nat Commun (2017) 8:15383-15383. DOI 10.1038/ncomms15383 · PubMed

Other PDB entries of the same protein (UniProt P00323 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5YOB 1.14 Å, Crystal Structure of flavodoxin without engineered disulfide bond
1F4P 1.3 Å, Y98W flavodoxin mutant 1.5A (D. Vulgaris)
1J8Q 1.35 Å, Low Temperature (100K) Crystal Structure of Flavodoxin D. vulgaris Wild-type at 1.35…
5YOE 1.35 Å, Crystal Structure of flavodoxin with engineered disulfide bond A43C-L74C
5YOG 1.42 Å, Crystal Structure of flavodoxin with engineered disulfide bond N14C-C93
1J9E 1.44 Å, Low Temperature (100K) Crystal Structure of Flavodoxin D. vulgaris S35C Mutant at 1.44…
5YOC 1.5 Å, Crystal Structure of flavodoxin with engineered disulfide bond C102-R125C
1AKR 1.58 Å, G61A oxidized flavodoxin mutant
1WSW 1.69 Å, Low Temperature (100K) Crystal Structure Of Flavodoxin Mutant S64C, dimer, semiquinone…
1XYY 1.7 Å, Low Temperature (100K) Crystal Structure Of Flavodoxin Mutant S64C, homodimer, oxidised…
1AKW 1.75 Å, G61L oxidized flavodoxin mutant
1XYV 1.79 Å, Low Temperature (100K) Crystal Structure Of Flavodoxin Mutant S64C, monomer, semiquinone…

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