2YA8 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NANA (TIGR4) IN COMPLEX WITH OSELTAMIVIR CARBOXYLATE

Authors :   H. Gut, G. Xu, G. L. Taylor, M. A. Walsh

Date :   18 Feb 11 (Deposition) - 27 Apr 11 (Release) - 08 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Hydrolase, Sialidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Gut, G. Xu, G. L. Taylor, M. A. Walsh
Structural Basis For Streptococcus Pneumoniae Nana Inhibition By Influenza Antivirals Zanamivir And Oseltamivir Carboxylate.
J. Mol. Biol. V. 409 496 2011
PubMed-ID: 21514303 | Reference-DOI: 10.1016/J.JMB.2011.04.016

Molecule 1 - NEURAMINIDASE A
	Chains	:	A, B
	EC Number	:	3.2.1.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 280-754
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	170187
	Other Details	:	THE SEQUENCE NUMBERING ABOVE CORRESPONDS TO THE CLOSEST UNIPROT SEQUENCE MATCH UNP B2DJD9. THE SEQUENCE NUMBERING FOR THE ENTRY SHOULD BE 303-777
	Strain	:	TIGR4
	Synonym	:	NANA

		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, 11)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
3	FMT	4	Ligand/Ion	FORMIC ACID
4	G39	2	Ligand/Ion	(3R,4R,5S)-4-(ACETYLAMINO)-5-AMINO-3-(PENTAN-3-YLOXY)CYCLOHEX-1-ENE-1-CARBOXYLIC ACID

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	FMT	1	Ligand/Ion	FORMIC ACID
4	G39	1	Ligand/Ion	(3R,4R,5S)-4-(ACETYLAMINO)-5-AMINO-3-(PENTAN-3-YLOXY)CYCLOHEX-1-ENE-1-CARBOXYLIC ACID

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	FMT	3	Ligand/Ion	FORMIC ACID
4	G39	1	Ligand/Ion	(3R,4R,5S)-4-(ACETYLAMINO)-5-AMINO-3-(PENTAN-3-YLOXY)CYCLOHEX-1-ENE-1-CARBOXYLIC ACID

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:332 , ASP A:357 , ILE A:401 , ASP A:402 , ILE A:427 , TYR A:575 , ARG A:648 , ARG A:706 , TYR A:737 , HOH A:2044 , HOH A:2312 , HOH A:2499 , HOH A:2500	BINDING SITE FOR RESIDUE G39 A1777
02	AC2	SOFTWARE	GLY A:501 , ASN A:502 , LYS A:509 , THR A:510 , SER A:511	BINDING SITE FOR RESIDUE CL A1778
03	AC3	SOFTWARE	TYR A:525 , SER A:526 , ASP A:527 , ASP A:528 , THR A:532 , HOH A:2501	BINDING SITE FOR RESIDUE FMT A1779
04	AC4	SOFTWARE	ILE A:328 , GLU A:350 , ARG A:352 , ASP A:360 , GLY A:362 , ASN A:383	BINDING SITE FOR RESIDUE EDO A1780
05	AC5	SOFTWARE	LEU A:337 , LYS A:338 , GLN A:741 , HOH A:2502 , HOH A:2503 , HOH A:2504	BINDING SITE FOR RESIDUE EDO A1781
06	AC6	SOFTWARE	ARG B:332 , ASP B:357 , ILE B:401 , ASP B:402 , ILE B:427 , TYR B:575 , ARG B:648 , ARG B:706 , TYR B:737 , HOH B:2301 , HOH B:2446 , HOH B:2447	BINDING SITE FOR RESIDUE G39 B1777
07	AC7	SOFTWARE	GLY B:501 , ASN B:502 , LYS B:509 , THR B:510 , SER B:511	BINDING SITE FOR RESIDUE CL B1778
08	AC8	SOFTWARE	GLU B:350 , ARG B:352 , ASP B:360 , GLY B:362 , ASN B:383 , HOH B:2448	BINDING SITE FOR RESIDUE EDO B1779
09	AC9	SOFTWARE	ASN A:610 , LYS A:617 , GLU B:435 , TYR B:450 , ARG B:514 , HOH B:2449	BINDING SITE FOR RESIDUE FMT B1780
10	BC1	SOFTWARE	LYS B:338 , GLN B:741 , HOH B:2429 , HOH B:2450 , HOH B:2451	BINDING SITE FOR RESIDUE FMT B1781
11	BC2	SOFTWARE	HIS B:566 , ARG B:569 , ASN B:719 , HOH B:2452	BINDING SITE FOR RESIDUE FMT B1782

(no "SS Bond" information available for 2YA8)

Asymmetric Unit

No.	Residues
1	Gly A:703	-	Pro A:704
2	Ala A:761	-	Tyr A:762
3	Gly B:703	-	Pro B:704
4	Ala B:761	-	Tyr B:762

(no "SAP(SNP)/Variant" information available for 2YA8)

(no "PROSITE Motif" information available for 2YA8)

(no "Exon" information available for 2YA8)

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:470
 aligned with NANA_STREE | P62575 from UniProtKB/Swiss-Prot  Length:1035

    Alignment length:470
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791
           NANA_STREE   322 ALTEKTDIFESGRNGKPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGNQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLNGSQSSRIIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWDFLSK 791
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..............eeeeeeeee.....eeeeeeee.........eeeeeeee..........eeee.........hhhhh..eeeeeeeee......eeeeeeee...hhhhhh.......eeee..eeeeeeee......eee....eee.....eeeeee.....hhhhh...eeee..eeeee..........ee.....eeeeeee..........eehhhhhh...eeeeee..ee.ee.........eeeeeeeee..hhhhhh.eeeeeee.......ee.......eee..eee......hhhhh...eeeee.....eeeee.....eeeeeee...........eeeeeee......eeeeeee..eeeeeeeee.....eeeeeeeeee.....eeeeeeeeeeeee...eeeeeee..eeeeeeee........eeeeeeeehhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ya8 A 307 ALTEKTDIFESGRNGNPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGDQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLDGSQSSRVIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWEFLSK 776
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776

Chain B from PDB  Type:PROTEIN  Length:470
 aligned with NANA_STREE | P62575 from UniProtKB/Swiss-Prot  Length:1035

    Alignment length:470
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791
           NANA_STREE   322 ALTEKTDIFESGRNGKPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGNQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLNGSQSSRIIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWDFLSK 791
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..............eeeeeeeee.....eeeeeeee.........eeeeeeee..........eeee.........hhhhh..eeeeeeeee......eeeeeeee...hhhhhh.......eeee..eeeeeeee......eee....eee.....eeeeee.....hhhhh...eeee..eeeee..........ee.....eeeeeee..........eehhhhhh......eee..ee.ee.........eeeeeee....hhhhhh.eeeeeee.......ee.......eee..eee......hhhhh...eeeee.....eeeee.....eeeeeee...........eeeeeee......eeeeeee..eeeeeeeee.....eeeeeeeeee.....eeeeeeeeeeeee...eeeeeee..eeeeeeee........eeeeeeeehhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ya8 B 307 ALTEKTDIFESGRNGNPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGDQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLDGSQSSRVIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWEFLSK 776
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776

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 2YA8)

(no "CATH Domain" information available for 2YA8)

(no "Pfam Domain" information available for 2YA8)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NANA_STREE | P62575)

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.
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:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ala A:761 - Tyr A:762	[ RasMol ]
		Ala B:761 - Tyr B:762	[ RasMol ]
		Gly A:703 - Pro A:704	[ RasMol ]
		Gly B:703 - Pro B:704	[ RasMol ]

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	2ya8
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	NANA_STREE \| P62575	:	2vvz 2ya4 2ya5 2ya6 2ya7 4c1x 4zxk 5kky

(no "Related Entries Specified in the PDB File" available for 2YA8)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (4, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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