3WLA - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SOPH NATIVE

Authors :   Y. Yang, T. P. Ko, J. H. Li, L. Liu, C. H. Huang, H. C. Chan, F. F. Ren, D. X. Ji J. Wang, R. T. Guo, J. Chen, G. C. Du

Date :   08 Nov 13 (Deposition) - 24 Sep 14 (Release) - 24 Sep 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Alpha/Beta-Hydrolase, Oxi-Polyvinyl Alcohol Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Yang, T. P. Ko, L. Liu, J. Li, C. H. Huang, H. C. Chan, F. Ren, D. Jia, A. H. -J. Wang, R. T. Guo, J. Chen, G. Du
Structural Insights Into Enzymatic Degradation Of Oxidized Polyvinyl Alcohol
Chembiochem V. 15 1882 2014
PubMed-ID: 25044912 | Reference-DOI: 10.1002/CBIC.201402166

Molecule 1 - OXIDIZED POLYVINYL ALCOHOL HYDROLASE
	Chains	:	A, B, C
	EC Number	:	3.7.1.7
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PPIC9K
	Expression System Strain	:	GS115
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Gene	:	OPH
	Organism Scientific	:	SPHINGOPYXIS
	Organism Taxid	:	292913
	Strain	:	113P3
	Synonym	:	OPH, OXIDIZED PVA HYDROLASE, BETA-DIKETONE HYDROLASE

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:50 , VAL A:51 , SER A:156 , TRP A:239 , HOH A:1012 , HOH A:1029 , ARG C:62	BINDING SITE FOR RESIDUE SO4 A 901
2	AC2	SOFTWARE	THR B:50 , VAL B:51 , SER B:156 , TRP B:239 , HIS B:279 , HOH B:523	BINDING SITE FOR RESIDUE SO4 B 401
3	AC3	SOFTWARE	ARG A:62 , THR C:50 , VAL C:51 , SER C:156 , HOH C:502 , HOH C:520 , HOH C:604	BINDING SITE FOR RESIDUE SO4 C 401
4	AC4	SOFTWARE	GLY A:91 , ALA A:92 , GLY A:93 , GLY C:91 , ALA C:92 , GLY C:93 , HOH C:559 , HOH C:610 , HOH C:624 , HOH C:642	BINDING SITE FOR RESIDUE SO4 C 402

Asymmetric Unit

No.	Residues
1	A:6	-	A:138
2	A:83	-	A:95
3	A:273	-	A:320
4	B:6	-	B:138
5	B:83	-	B:95
6	B:273	-	B:320
7	C:6	-	C:138
8	C:83	-	C:95
9	C:273	-	C:320

Asymmetric Unit

No.	Residues
1	Tyr A:217	-	Pro A:218
2	Pro A:243	-	Pro A:244
3	Tyr B:217	-	Pro B:218
4	Pro B:243	-	Pro B:244
5	Tyr C:217	-	Pro C:218
6	Pro C:243	-	Pro C:244

(no "SAP(SNP)/Variant" information available for 3WLA)

(no "PROSITE Motif" information available for 3WLA)

(no "Exon" information available for 3WLA)

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:329
 aligned with OPH_SPHS1 | Q588Z2 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:329
                                    45        55        65        75        85        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         
            OPH_SPHS1    36 SEWACPEGFTPKAGLNTDFPSDGKKRAFVVVPPKDSAGGAPVWVPMVGTVEATNWNLNVPRSGNNAKLAEHGYMVISPVRQCAEQDPNLGAGACNGVGKDGWTWNPWNDGRAPDASGDKYKTDAGDDVRFLEAMVRCVGTKWKLDRKRLFLGGISAGGTMTNRALLFDSEFWAGGMPISGEWYSTKDDGSTVPFQETRKMVAAAPAKIWQGRVGPYPLPSKLDPMVVITVWGGEKDLWDCGPPLGLCSDYRPTTQASSNYFSSISNVVHVACSATHGHMWPQVNTDAFNLWALNTMASHPKGSSPKDFKLTAPPEGYSCKIGRFTDHYK 364
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeee..eeeeeeee........eeeeeee.....hhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh......hhhhh..................hhhhhhhhh..hhhhhhhhhhhhhhh....eeeeeeeeeeehhhhhhhhhhhhhh.....eeeee..............hhhhhhhhhhhh....................eeeeeee.....eee......eeeehhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhh.....hhhhh.........eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wla A   2 SEWACPEGFTPKAGLNTDFPSDGKKRAFVVVPPKDSAGGAPVWVPMVGTVEATNWNLNVPRSGNNAKLAEHGYMVISPVRQCAEQDPNLGAGACNGVGKDGWTWNPWNDGRAPDASGDKYKTDAGDDVRFLEAMVRCVGTKWKLDRKRLFLGGISAGGTMTNRALLFDSEFWAGGMPISGEWYSTKDDGSTVPFQETRKMVAAAPAKIWQGRVGPYPLPSKLDPMVVITVWGGEKDLWDCGPPLGLCSDYRPTTQASSNYFSSISNVVHVACSATHGHMWPQVNTDAFNLWALNTMASHPKGSSPKDFKLTAPPEGYSCKIGRFTDHYK 330
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321

Chain B from PDB  Type:PROTEIN  Length:329
 aligned with OPH_SPHS1 | Q588Z2 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:329
                                    45        55        65        75        85        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         
            OPH_SPHS1    36 SEWACPEGFTPKAGLNTDFPSDGKKRAFVVVPPKDSAGGAPVWVPMVGTVEATNWNLNVPRSGNNAKLAEHGYMVISPVRQCAEQDPNLGAGACNGVGKDGWTWNPWNDGRAPDASGDKYKTDAGDDVRFLEAMVRCVGTKWKLDRKRLFLGGISAGGTMTNRALLFDSEFWAGGMPISGEWYSTKDDGSTVPFQETRKMVAAAPAKIWQGRVGPYPLPSKLDPMVVITVWGGEKDLWDCGPPLGLCSDYRPTTQASSNYFSSISNVVHVACSATHGHMWPQVNTDAFNLWALNTMASHPKGSSPKDFKLTAPPEGYSCKIGRFTDHYK 364
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeee..eeeeeeee........eeeeeee.....hhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh......hhhhh..................hhhhhhhhh..hhhhhhhhhhhhhhh....eeeeeeeeeeehhhhhhhhhhhhhh.....eeeee..............hhhhhhhhhhhh....................eeeeeee.....eee......eeeehhhhhhhhhhhhhhh..eeeeeee..........hhhhhhhhhhhhhhh.....hhhhh.........eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wla B   2 SEWACPEGFTPKAGLNTDFPSDGKKRAFVVVPPKDSAGGAPVWVPMVGTVEATNWNLNVPRSGNNAKLAEHGYMVISPVRQCAEQDPNLGAGACNGVGKDGWTWNPWNDGRAPDASGDKYKTDAGDDVRFLEAMVRCVGTKWKLDRKRLFLGGISAGGTMTNRALLFDSEFWAGGMPISGEWYSTKDDGSTVPFQETRKMVAAAPAKIWQGRVGPYPLPSKLDPMVVITVWGGEKDLWDCGPPLGLCSDYRPTTQASSNYFSSISNVVHVACSATHGHMWPQVNTDAFNLWALNTMASHPKGSSPKDFKLTAPPEGYSCKIGRFTDHYK 330
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321

Chain C from PDB  Type:PROTEIN  Length:329
 aligned with OPH_SPHS1 | Q588Z2 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:329
                                    45        55        65        75        85        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         
            OPH_SPHS1    36 SEWACPEGFTPKAGLNTDFPSDGKKRAFVVVPPKDSAGGAPVWVPMVGTVEATNWNLNVPRSGNNAKLAEHGYMVISPVRQCAEQDPNLGAGACNGVGKDGWTWNPWNDGRAPDASGDKYKTDAGDDVRFLEAMVRCVGTKWKLDRKRLFLGGISAGGTMTNRALLFDSEFWAGGMPISGEWYSTKDDGSTVPFQETRKMVAAAPAKIWQGRVGPYPLPSKLDPMVVITVWGGEKDLWDCGPPLGLCSDYRPTTQASSNYFSSISNVVHVACSATHGHMWPQVNTDAFNLWALNTMASHPKGSSPKDFKLTAPPEGYSCKIGRFTDHYK 364
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeee..eeeeeeee........eeeeeee.....hhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh......hhhhh..................hhhhhhhhh..hhhhhhhhhhhhhhh....eeeeeeeeeeehhhhhhhhhhhhhh.....eeeee..............hhhhhhhhhhhh....................eeeeeee.....eee......eeeehhhhhhhhhhhhhhh..eeeeeee..........hhhhhhhhhhhhhhh.....hhhhh.........eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wla C   2 SEWACPEGFTPKAGLNTDFPSDGKKRAFVVVPPKDSAGGAPVWVPMVGTVEATNWNLNVPRSGNNAKLAEHGYMVISPVRQCAEQDPNLGAGACNGVGKDGWTWNPWNDGRAPDASGDKYKTDAGDDVRFLEAMVRCVGTKWKLDRKRLFLGGISAGGTMTNRALLFDSEFWAGGMPISGEWYSTKDDGSTVPFQETRKMVAAAPAKIWQGRVGPYPLPSKLDPMVVITVWGGEKDLWDCGPPLGLCSDYRPTTQASSNYFSSISNVVHVACSATHGHMWPQVNTDAFNLWALNTMASHPKGSSPKDFKLTAPPEGYSCKIGRFTDHYK 330
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 3WLA)

(no "CATH Domain" information available for 3WLA)

(no "Pfam Domain" information available for 3WLA)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (OPH_SPHS1 | Q588Z2)

molecular function
	GO:0047699	beta-diketone hydrolase activity	Catalysis of the reaction: H(2)O + nonane-4,6-dione = butanoate + H(+) + pentan-2-one.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
cellular component
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric Unit
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	Cis Peptide Bonds
		Pro A:243 - Pro A:244	[ RasMol ]
		Pro B:243 - Pro B:244	[ RasMol ]
		Pro C:243 - Pro C:244	[ RasMol ]
		Tyr A:217 - Pro A:218	[ RasMol ]
		Tyr B:217 - Pro B:218	[ RasMol ]
		Tyr C:217 - Pro C:218	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
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		Biological Unit 3	[ Jena3D ]

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	3wla
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	OPH_SPHS1 \| Q588Z2
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	3.7.1.7
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(no "Entries Sharing at Least One Protein Chain" available for 3WLA)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (9, 9)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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