4UZ6 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM V - SOS COMPLEX - 1.9A

Authors :   M. Zebisch, E. Y. Jones

Date :   04 Sep 14 (Deposition) - 25 Feb 15 (Release) - 18 Mar 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Hydrolase, Wnt, Esterase, Extracellular, Alpha/Beta Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Kakugawa, P. F. Langton, M. Zebisch, S. A. Howell, T. Chang, Y. Liu, T. Feizi, G. Bineva, N. O'Reilly, A. P. Snijders, E. Y. Jones, J. Vincen
Notum Deacylates Wnt Proteins To Suppress Signalling Activity.
Nature V. 519 187 2015
PubMed-ID: 25731175 | Reference-DOI: 10.1038/NATURE14259

Molecule 1 - PROTEIN NOTUM HOMOLOG
	Chains	:	A, B
	EC Number	:	3.1.1.1
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293T
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PHLSEC
	Expression System Taxid	:	9606
	Fragment	:	RESIDUES 81-451
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	GLYCOSYLATED AT N96

		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 (3, 6)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SCR	2	Ligand/Ion	SUCROSE OCTASULFATE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SCR	1	Ligand/Ion	SUCROSE OCTASULFATE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SCR	1	Ligand/Ion	SUCROSE OCTASULFATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:117 , ARG A:118 , ARG A:119 , ASN A:174 , LYS A:224 , VAL A:225 , HIS A:412 , ASP A:415 , ARG A:416 , HIS A:419 , HOH A:2013 , HOH A:2112 , HOH A:2118 , HOH A:2119 , HOH A:2120 , HOH A:2121 , HIS B:276 , THR B:288 , GLU B:289 , ARG B:292 , HOH B:2072	BINDING SITE FOR RESIDUE SCR A1453
2	AC2	SOFTWARE	LYS A:272 , HIS A:276 , ALA A:286 , HOH A:2069 , HOH A:2073 , HOH A:2077 , HOH A:2079 , ARG B:119 , LYS B:224 , VAL B:225 , GLN B:258 , ASP B:415 , ARG B:416 , HIS B:419 , HOH B:2055	BINDING SITE FOR RESIDUE SCR B1453
3	AC3	SOFTWARE	ARG B:90	BINDING SITE FOR RESIDUE CL B1454
4	AC4	SOFTWARE	ARG A:218	BINDING SITE FOR RESIDUE CL A1454
5	AC5	SOFTWARE	ASN A:96 , VAL A:99 , SER A:193 , PRO B:447	BINDING SITE FOR MONO-SACCHARIDE NAG A1452 BOUND TO ASN A 96
6	AC6	SOFTWARE	ASN B:96 , SER B:98 , VAL B:99 , SER B:193 , MET B:203	BINDING SITE FOR MONO-SACCHARIDE NAG B1452 BOUND TO ASN B 96

Asymmetric Unit

No.	Residues
1	A:101	-	A:183
2	A:130	-	A:136
3	A:279	-	A:285
4	A:306	-	A:318
5	A:386	-	A:449
6	A:413	-	A:432
7	A:440	-	A:445
8	B:101	-	B:183
9	B:130	-	B:136
10	B:279	-	B:285
11	B:306	-	B:318
12	B:386	-	B:449
13	B:413	-	B:432
14	B:440	-	B:445

(no "Cis Peptide Bond" information available for 4UZ6)

(no "SAP(SNP)/Variant" information available for 4UZ6)

(no "PROSITE Motif" information available for 4UZ6)

(no "Exon" information available for 4UZ6)

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:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..............eeeee......eeeeee.......hhhhhhhhhhhhhhhh.......ee..hhhhh............eeeee......................hhhhhhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhhhhhh.....eeeeeee.....................hhhhhhhhhhhhhh...hhhhhh.....hhhhhhhhhhhhhhh...eeee...eehhhhhhh.....hhhhhhhhhhhhhhhhhhhh....eee...ee.....hhhhhh.ee..eehhhhhhhhhhhhh....eee.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uz6 A  86 NEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHGCPVHLVDSCPWPHCNPSCPT 451
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345    || 359       369       379       389       399       409       419|      440       450 
                                                                                                                                                                                                                                                                                                  350|                                                             419|                    
                                                                                                                                                                                                                                                                                                   355                                                              431

Chain B from PDB  Type:PROTEIN  Length:355
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..............eeeee......eeeeee.......hhhhhhhhhhhhhhhhh......ee..hhhhh............eeeee......................hhhhhhhhhhhhhh..hhhhh.eeeeeeehhhhhhhhhhhhhhhhhhhhh.....eeeeeee.....................hhhhhhhhhhhhhh...hhhhhh.....hhhhhhhhhhhhhhh...eeee...eehhhhhhh.........hhhhhhhhhhhhhhhhhhh.....eee...ee............ee..eehhhhhhhhhhhhhh...eee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uz6 B  86 NEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDCPVHLVDSCPWPHCNPSCPT 451
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415    || 436       446     
                                                                                                                                                                                                                                                                                                                                                                        420|                   
                                                                                                                                                                                                                                                                                                                                                                         432

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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 4UZ6)

(no "CATH Domain" information available for 4UZ6)

(no "Pfam Domain" information available for 4UZ6)

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4uz6)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	4uz6
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	3.1.1.1
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UniProtKB/Swiss-Prot
	NOTUM_HUMAN \| Q6P988	:	4uyu 4uyw 4uyz 4uz1 4uz5 4uz7 4uz9 4uza 4uzl 4uzq 4wbh

4uyu	STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM I IODIDE COMPLEX - 2.3A
4uyw	STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM I HEPARIN FRAGMENT COMPLEX - 1.7A
4uyz	STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM II - 2.8A
4uz1	STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM III - 1.4A
4uz5	STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM IV - 2.1A
4uz7	STRUCTURE OF THE WNT DEACETYLASE NOTUM - CRYSTAL FORM VII - SOS COMPLEX - 2.2A
4uz9	STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM VII - SOS COMPLEX - 2.2A
4uza	STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM VIII - PHOSPHATE COMPLEX - 2.4A
4uzj	STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM III - 1.4A
4uzk	STRUCTURE OF THE WNT DEACYLASE NOTUM FROM DROSOPHILA - CRYSTAL FORM II - 1.9A
4uzl	STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM I MYRISTOLEATE COMPLEX - 2.1A
4uzq	STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH O-PALMITOLEOYL SERINE - CRYSTAL FORM IX - 1.5A

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (14, 14)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

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