5L7I - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF HUMAN SMOOTHENED IN COMPLEX WITH VISMODEGIB

Authors :   E. X. B. Byrne, R. Sircar, P. S. Miller, G. Hedger, G. Luchetti, S. Nachte M. D. Tully, L. Mydock-Mcgrane, D. F. Covey, R. F. Rambo, M. S. P. Sansom S. Newstead, R. Rohatgi, C. Siebold

Date :   03 Jun 16 (Deposition) - 20 Jul 16 (Release) - 10 Aug 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   G Protein Coupled Receptor, Morphogen Signaling, Membrane Protein, Hedgehog Signaling, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. F. Byrne, R. Sircar, P. S. Miller, G. Hedger, G. Luchetti, S. Nachtergaele, M. D. Tully, L. Mydock-Mcgrane, D. F. Covey, R. P. Rambo, M. S. Sansom, S. Newstead, R. Rohatgi, C. Siebold
Structural Basis Of Smoothened Regulation By Its Extracellular Domains.
Nature V. 535 517 2016
PubMed-ID: 27437577 | Reference-DOI: 10.1038/NATURE18934

Molecule 1 - SMOOTHENED HOMOLOG,SOLUBLE CYTOCHROME B562,SMOOTHENED HOMOLOG
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK-293S-GNTI-
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PHLSEC
	Expression System Taxid	:	9606
	Gene	:	SMO, SMOH, CYBC
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS, ESCHERICHIA COLI
	Organism Taxid	:	9606, 562
	Other Details	:	HUMAN SMOOTHENED WITH A SOLUBLE E. COLI CYTOCHROME B562 PROTEIN REPLACING SMOOTHENED RESIDUES 429 TO 444
	Synonym	:	SMO,PROTEIN GX,CYTOCHROME B-562,SMO,PROTEIN GX

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 6)

No.	Name	Count	Type	Full Name
1	MPG	2	Ligand/Ion	[(Z)-OCTADEC-9-ENYL] (2R)-2,3-BIS(OXIDANYL)PROPANOATE
2	NA	1	Ligand/Ion	SODIUM ION
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	VIS	2	Ligand/Ion	2-CHLORANYL-~{N}-(4-CHLORANYL-3-PYRIDIN-2-YL-PHENYL)-4-METHYLSULFONYL-BENZAMIDE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	MPG	-1	Ligand/Ion	[(Z)-OCTADEC-9-ENYL] (2R)-2,3-BIS(OXIDANYL)PROPANOATE
2	NA	-1	Ligand/Ion	SODIUM ION
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	VIS	1	Ligand/Ion	2-CHLORANYL-~{N}-(4-CHLORANYL-3-PYRIDIN-2-YL-PHENYL)-4-METHYLSULFONYL-BENZAMIDE

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	MPG	2	Ligand/Ion	[(Z)-OCTADEC-9-ENYL] (2R)-2,3-BIS(OXIDANYL)PROPANOATE
2	NA	-1	Ligand/Ion	SODIUM ION
3	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	VIS	1	Ligand/Ion	2-CHLORANYL-~{N}-(4-CHLORANYL-3-PYRIDIN-2-YL-PHENYL)-4-METHYLSULFONYL-BENZAMIDE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:221 , TRP A:281 , ASP A:384 , SER A:387 , TYR A:394 , ARG A:400 , GLN A:477 , TRP A:480 , GLU A:518 , ASN A:521 , LEU A:522	binding site for residue VIS A 1202
2	AC2	SOFTWARE	THR B:90 , LEU B:91 , ALA B:93 , SER B:96 , ASP B:97	binding site for residue NA B 1201
3	AC3	SOFTWARE	LEU B:221 , TRP B:281 , ASP B:384 , SER B:387 , TYR B:394 , ARG B:400 , ASP B:473 , GLN B:477 , TRP B:480 , GLU B:518 , LEU B:522	binding site for residue VIS B 1202
4	AC4	SOFTWARE	TRP A:256 , LEU B:376 , ALA B:377	binding site for residue MPG B 1203
5	AC5	SOFTWARE	MET A:286 , TRP B:256 , TYR B:269 , HIS B:361 , TRP B:365	binding site for residue MPG B 1204
6	AC6	SOFTWARE	GLU A:160 , LEU A:489 , ASN A:493	binding site for Mono-Saccharide NAG A 1201 bound to ASN A 493

Asymmetric Unit

No.	Residues
1	A:64	-	A:178
2	A:70	-	A:134
3	A:78	-	A:127
4	A:118	-	A:154
5	A:147	-	A:169
6	A:193	-	A:213
7	A:217	-	A:295
8	A:314	-	A:390
9	A:490	-	A:507
10	B:64	-	B:178
11	B:70	-	B:134
12	B:78	-	B:127
13	B:118	-	B:154
14	B:147	-	B:169
15	B:193	-	B:213
16	B:217	-	B:295
17	B:314	-	B:390
18	B:490	-	B:507

Asymmetric Unit

No.	Residues
1	Val A:195	-	Pro A:196
2	Tyr A:262	-	Pro A:263
3	Glu A:305	-	Pro A:306
4	Val B:195	-	Pro B:196
5	Tyr B:262	-	Pro B:263
6	Glu B:305	-	Pro B:306

(no "SAP(SNP)/Variant" information available for 5L7I)

(no "PROSITE Motif" information available for 5L7I)

(no "Exon" information available for 5L7I)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:564
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eee...ee..............ee.........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......eee..hhhhhhhhhh.hhhhhhhh..hhhhh............................eee..hhhhh......eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....eeee...hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5l7i A   57 PPPPLSHCGRAAPCEPLRYNVCLGSVLPYGATSTLLAGDSDSQEEAHGKLVLWSGLRNAPRCWAVIQPLLCAVYMPKCENDRVELPSRTLCQATRGPCAIVERERGWPDFLRCTPDRFPEGCTNEVQNIKFNSSGQCEVPLVRTDNPKSWYEDVEGCGIQCQNPLFTEAEHQDMHSYIAAFGAVTGLCTLFTLATFVADWRNSNRYPAVILFYVNACFFVGSIGWLAQFMDGARREIVCRADGTMRLGEPTSNETLSCVIIFVIVYYALMAGFVWFVVLTYAWHTSFLSGKTSYFHLLTWSLPFVLTVAILAVAQVDGDSVSGICFVGYKNYRYRAGFVLAPIGLVLIVGGYFLIRGVMTLFSARRQLADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLERARSTLSKINETMLRLGIFGFLAFGFVLITFSCHFYDFFNQAEWERSFRDYVLCQANVTDCEIKNRPSLLVEKINLFAMFGTGIAMSTWVWTKATLLIWRRTWCR  551
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336      |355       365       375       385       395       405       415       425  ||  1017      1027      1037      1047      1057|     1083      1093      1103      1113      1123       447       457       467       477       487       507       517       527       537       547    
                                                                                                                                                                                                                                                                                                                        343|                                                                        428|                                          1057|                                                     1131|                                              495|                                             
                                                                                                                                                                                                                                                                                                                         353                                                                        1011                                           1074                                                       446                                               506

Chain B from PDB  Type:PROTEIN  Length:572
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee...ee..............ee.........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......eee..hhhhhhhhhh.hhhhhhhh..hhhhh............................eee..hhh.ee..eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh.eeee....eeee...hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5l7i B   58 PPPLSHCGRAAPCEPLRYNVCLGSVLPYGATSTLLAGDSDSQEEAHGKLVLWSGLRNAPRCWAVIQPLLCAVYMPKCENDRVELPSRTLCQATRGPCAIVERERGWPDFLRCTPDRFPEGCTNEVQNIKFNSSGQCEVPLVRTDNPKSWYEDVEGCGIQCQNPLFTEAEHQDMHSYIAAFGAVTGLCTLFTLATFVADWRNSNRYPAVILFYVNACFFVGSIGWLAQFMDGARREIVCRADGTMRLGEPTSNETLSCVIIFVIVYYALMAGFVWFVVLTYAWHTSFKALGTTYQPLSGKTSYFHLLTWSLPFVLTVAILAVAQVDGDSVSGICFVGYKNYRYRAGFVLAPIGLVLIVGGYFLIRGVMTLFSARRQLADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLERARSTLSKINETMLRLGIFGFLAFGFVLITFSCHFYDFFNQAEWERSFRDYVLCQANVTDCEIKNRPSLLVEKINLFAMFGTGIAMSTWVWTKATLLIWRRTWCRL  552
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427||    1019      1029      1039      1049      1076      1086      1096      1106      1116      1126    || 450       460       470       480       490    || 510       520       530       540       550  
                                                                                                                                                                                                                                                                                                                                                                                                            428|                                          1057|                                                    1131|                                              495|                                              
                                                                                                                                                                                                                                                                                                                                                                                                            1011                                           1075                                                      446                                               506

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 5L7I)

(no "CATH Domain" information available for 5L7I)

(no "Pfam Domain" information available for 5L7I)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Glu A:305 - Pro A:306	[ RasMol ]
		Glu B:305 - Pro B:306	[ RasMol ]
		Tyr A:262 - Pro A:263	[ RasMol ]
		Tyr B:262 - Pro B:263	[ RasMol ]
		Val A:195 - Pro A:196	[ RasMol ]
		Val B:195 - Pro B:196	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]

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(no "Related Entries Specified in the PDB File" available for 5L7I)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

SS Bonds (18, 18)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (107, 107)

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