3NSS - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   THE 2009 PANDEMIC H1N1 NEURAMINIDASE N1 LACKS THE 150-CAVITY IN ITS ACTIVE SITES

Authors :   Q. Li, J. X. Qi, W. Zhang, C. J. Vavricka, Y. Shi, G. F. Gao

Date :   02 Jul 10 (Deposition) - 22 Sep 10 (Release) - 26 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   6-Bladed Beta-Propeller, Hydrolase, Calcium Binding, Glycosylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Q. Li, J. X. Qi, W. Zhang, C. J. Vavricka, Y. Shi, J. H. Wei, E. G. Feng, J. S. Shen, J. L. Chen, D. Liu, J. H. He, J. H. Yan, H. Liu, H. L. Jiang, M. K. Teng, X. B. Li, G. F. Gao
The 2009 Pandemic H1N1 Neuraminidase N1 Lacks The 150-Cavit In Its Active Site
Nat. Struct. Mol. Biol. V. 17 1266 2010
PubMed-ID: 20852645 | Reference-DOI: 10.1038/NSMB.1909

Molecule 1 - NEURAMINIDASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Cell Line	:	SF9
	Expression System Plasmid	:	PACGP67-B
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	UNP RESIDUES 82-469
	Gene	:	NA
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	641501
	Strain	:	A/CALIFORNIA/04/2009 H1N1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 16)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	CA	5	Ligand/Ion	CALCIUM ION
3	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (3, 22)

No.	Name	Count	Type	Full Name
1	ACT	8	Ligand/Ion	ACETATE ION
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MAN	4	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	10	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:146 , NAG A:502 , HOH A:617 , HOH A:834 , HOH A:891	BINDING SITE FOR RESIDUE NAG A 501
02	AC2	SOFTWARE	NAG A:501 , MAN A:503 , ASN B:329	BINDING SITE FOR RESIDUE NAG A 502
03	AC3	SOFTWARE	NAG A:502 , MAN A:504 , HOH B:683	BINDING SITE FOR RESIDUE MAN A 503
04	AC4	SOFTWARE	MAN A:503 , ARG B:327 , ASP B:330 , ARG B:364 , LYS B:366 , GLU B:375	BINDING SITE FOR RESIDUE MAN A 504
05	AC5	SOFTWARE	ALA A:86 , ASN A:88 , HOH A:718 , HOH A:745 , HOH A:768 , HOH A:843	BINDING SITE FOR RESIDUE NAG A 505
06	AC6	SOFTWARE	ASP A:293 , GLY A:297 , ASP A:324 , GLY A:345 , ASN A:347 , HOH A:476	BINDING SITE FOR RESIDUE CA A 601
07	AC7	SOFTWARE	ASP A:379 , ASN A:381 , ASP A:387 , ASN A:389 , HOH A:493 , HOH A:565	BINDING SITE FOR RESIDUE CA A 602
08	AC8	SOFTWARE	HOH B:488 , HOH B:902 , HOH B:903 , HOH B:905	BINDING SITE FOR RESIDUE CA A 603
09	AC9	SOFTWARE	HOH A:53 , GLU A:276 , GLU A:277 , ARG A:292 , HOH A:888	BINDING SITE FOR RESIDUE ACT A 1
10	BC1	SOFTWARE	VAL A:94 , TRP A:361 , HOH A:798	BINDING SITE FOR RESIDUE ACT A 471
11	BC2	SOFTWARE	ASN A:272 , HOH A:875	BINDING SITE FOR RESIDUE ACT A 472
12	BC3	SOFTWARE	ASN B:146 , HOH B:872	BINDING SITE FOR RESIDUE NAG B 501
13	BC4	SOFTWARE	ASN B:88 , HOH B:565	BINDING SITE FOR RESIDUE NAG B 502
14	BC5	SOFTWARE	HOH B:3 , ASP B:293 , GLY B:297 , ASP B:324 , GLY B:345 , ASN B:347	BINDING SITE FOR RESIDUE CA B 601
15	BC6	SOFTWARE	HOH B:56 , ASP B:379 , ASN B:381 , ASP B:387 , ASN B:389 , HOH B:575	BINDING SITE FOR RESIDUE CA B 602
16	BC7	SOFTWARE	VAL B:94 , TRP B:361	BINDING SITE FOR RESIDUE ACT B 1

Asymmetric Unit

No.	Residues
1	A:92	-	A:417
2	A:124	-	A:129
3	A:183	-	A:230
4	A:232	-	A:237
5	A:278	-	A:291
6	A:280	-	A:289
7	A:318	-	A:336
8	A:421	-	A:447
9	B:92	-	B:417
10	B:124	-	B:129
11	B:183	-	B:230
12	B:232	-	B:237
13	B:278	-	B:291
14	B:280	-	B:289
15	B:318	-	B:336
16	B:421	-	B:447

Asymmetric Unit

No.	Residues
1	Asn A:325	-	Pro A:326
2	Arg A:430	-	Pro A:431
3	Leu A:464	-	Pro A:465
4	Asn B:325	-	Pro B:326
5	Arg B:430	-	Pro B:431
6	Leu B:464	-	Pro B:465

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

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

(no "Exon" information available for 3NSS)

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:387
 aligned with C3W5S3_I09A0 | C3W5S3 from UniProtKB/TrEMBL  Length:469

    Alignment length:387
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       
        C3W5S3_I09A0     82 SVKLAGNSSLCPVSGWAIYSKDNSVRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQDIVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTID  468
               SCOP domains d3nssa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhhh....eeeeeeeeee....eeeeeeeeeee..hhhhh..........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee..............eee..eeeeeeee.......eeeeeeee..eeeeeee........eeeeeeee..eeeeeee........eeeee.....eeeee.................................eeee..eeeeee.......eeeeeeee............eeeeeeeeeee...eeeeeehhhhhh....eeeeeeeeeee........eeeeeeeeeee.................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3nss A   82 SVKLAGNSSLCPVSGWAIYSKDNSVRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQDIVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTID  469
                                    91       101       111       121       131       141       151       161       170       180       190       200       210       220       230       240       250       260       270       280       290       300     ||311       321       331 ||||  344       354       364       374       384       395       405      412C|      421       431 ||    442       452       462       
                                                                                                                 169A                                                                                                                                      306|                      333|||                                                  392|               412A|||                  433|                                  
                                                                                                                                                                                                                                                            308                       335||                                                   394                412B||                   435                                  
                                                                                                                                                                                                                                                                                       336|                                                                       412C|                                                        
                                                                                                                                                                                                                                                                                        339                                                                        412D

Chain B from PDB  Type:PROTEIN  Length:387
 aligned with C3W5S3_I09A0 | C3W5S3 from UniProtKB/TrEMBL  Length:469

    Alignment length:387
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       
        C3W5S3_I09A0     82 SVKLAGNSSLCPVSGWAIYSKDNSVRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQDIVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTID  468
               SCOP domains d3nssb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Neur-3nssB01 B:82-466                                                                                                                                                                                                                                                                                                                                                                           --- Pfam domains (1)
           Pfam domains (2) Neur-3nssB02 B:82-466                                                                                                                                                                                                                                                                                                                                                                           --- Pfam domains (2)
         Sec.struct. author ..............eeeeeee.hhhhhhh....eeeeeeeeee....eeeeeeeeeee..hhhhh..........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee..............eee..eeeeeeee.......eeeeeeee..eeeeeee........eeeeeeee..eeeeeee........eeeee.....eeeee.................................eeee..eeeeee.......eeeeeeee............eeeeeeeeeee...eeeeeehhhhhh....eeeeeeeeeee........eeeeeeeeeee.................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3nss B   82 SVKLAGNSSLCPVSGWAIYSKDNSVRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQDIVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTID  469
                                    91       101       111       121       131       141       151       161       170       180       190       200       210       220       230       240       250       260       270       280       290       300     ||311       321       331 ||||  344       354       364       374       384       395       405      412C|      421       431 ||    442       452       462       
                                                                                                                 169A                                                                                                                                      306|                      333|||                                                  392|               412A|||                  433|                                  
                                                                                                                                                                                                                                                            308                       335||                                                   394                412B||                   435                                  
                                                                                                                                                                                                                                                                                       336|                                                                       412C|                                                        
                                                                                                                                                                                                                                                                                        339                                                                        412D

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: 6-bladed beta-propeller (327)

Superfamily: Sialidases (238)

Family: automated matches (54)

Protein domain: automated matches (54)

Influenza A virus [TaxId: 641501] (5)

1a	d3nssa_	A:
1b	d3nssb_	B:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Sialidase (56)

Family: Neur (42)

Influenza A virus (strain swl A/California/04/2009 H1N1) (1)

1a	Neur-3nssB01	B:82-466
1b	Neur-3nssB02	B:82-466

Asymmetric Unit(hide GO term definitions)

Chain A,B (C3W5S3_I09A0 | C3W5S3)

molecular function
	GO:0052794	exo-alpha-(2->3)-sialidase activity	Catalysis of the hydrolysis of alpha-(2->3)-glycosidic linkages of terminal sialic residues in substrates.
	GO:0052795	exo-alpha-(2->6)-sialidase activity	Catalysis of the hydrolysis of alpha-(2->6)-glycosidic linkages of terminal sialic residues in substrates.
	GO:0052796	exo-alpha-(2->8)-sialidase activity	Catalysis of the hydrolysis of alpha-(2->8)-glycosidic linkages of terminal sialic residues in substrates.
	GO:0004308	exo-alpha-sialidase activity	Catalysis of the hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
	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.
	GO:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Asymmetric Unit
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	Cis Peptide Bonds
		Arg A:430 - Pro A:431	[ RasMol ]
		Arg B:430 - Pro B:431	[ RasMol ]
		Asn A:325 - Pro A:326	[ RasMol ]
		Asn B:325 - Pro B:326	[ RasMol ]
		Leu A:464 - Pro A:465	[ RasMol ]
		Leu B:464 - Pro B:465	[ RasMol ]

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3beq	1918 HUMAN N1 NEURAMINIDASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 16)

Sites (16, 16)

SS Bonds (16, 16)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Related Entries Specified in the PDB File