2QWB - JenaLib

Title :   THE X-RAY STRUCTURE OF A COMPLEX OF SIALIC ACID AND A DRUG RESISTANT VARIANT R292K OF TERN N9 INFLUENZA VIRUS NEURAMINIDASE

Authors :   J. N. Varghese

Date :   07 Apr 98 (Deposition) - 11 Nov 98 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Neuraminidase, Influenza Protein, Drug Resistant Variant, Sialic Acid, Second Binding Site, Glycosylated Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. N. Varghese, P. W. Smith, S. L. Sollis, T. J. Blick, A. Sahasrabudhe, J. L. Mckimm-Breschkin, P. M. Colman
Drug Design Against A Shifting Target: A Structural Basis For Resistance To Inhibitors In A Variant Of Influenza Viru Neuraminidase.
Structure V. 6 735 1998
PubMed-ID: 9655825 | Reference-DOI: 10.1016/S0969-2126(98)00075-6
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 14)

Sites (14, 14)

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:199 , ASN A:200 , LEU A:453 , GLY A:454 , GLN A:455 , NAG A:470B , HOH A:1079W , HOH A:1229K , HOH A:1293N , HOH A:1342R , HOH A:1369R	BINDING SITE FOR RESIDUE NAG A 469A
02	AC2	SOFTWARE	GLN A:392 , GLY A:394 , GLN A:455 , NAG A:469A , BMA A:471C , HOH A:1026W , HOH A:1165F , HOH A:1214K , HOH A:1229K , HOH A:1293N	BINDING SITE FOR RESIDUE NAG A 470B
03	AC3	SOFTWARE	LEU A:377 , THR A:391 , GLN A:392 , GLY A:394 , NAG A:470B , MAN A:472D , MAN A:475G , HOH A:1075W , HOH A:1214K	BINDING SITE FOR RESIDUE BMA A 471C
04	AC4	SOFTWARE	ARG A:364 , GLU A:375 , BMA A:471C , MAN A:473E , MAN A:474F , HOH A:1148F , HOH A:1284N	BINDING SITE FOR RESIDUE MAN A 472D
05	AC5	SOFTWARE	ASP A:330 , ARG A:364 , LYS A:389 , PRO A:390 , MAN A:472D , MAN A:474F , HOH A:1261M , HOH A:1357R	BINDING SITE FOR RESIDUE MAN A 473E
06	AC6	SOFTWARE	ARG A:327 , ASN A:329 , ASP A:330 , ARG A:364 , ILE A:366 , ILE A:368 , MAN A:472D , MAN A:473E , HOH A:1074W , HOH A:1145F , HOH A:1350R	BINDING SITE FOR RESIDUE MAN A 474F
07	AC7	SOFTWARE	BMA A:471C , HOH A:1210K , HOH A:1211K , HOH A:1330Q	BINDING SITE FOR RESIDUE MAN A 475G
08	AC8	SOFTWARE	ASP A:83 , PHE A:84 , ASN A:86 , ASN A:234 , NAG A:477B , HOH A:1180G , HOH A:1341R	BINDING SITE FOR RESIDUE NAG A 476A
09	AC9	SOFTWARE	ASP A:83 , NAG A:476A , HOH A:1341R	BINDING SITE FOR RESIDUE NAG A 477B
10	BC1	SOFTWARE	ASN A:146 , TRP A:437 , HOH A:1164F	BINDING SITE FOR RESIDUE NAG A 478A
11	BC2	SOFTWARE	ARG A:118 , GLU A:119 , ASP A:151 , ARG A:152 , ALA A:246 , GLU A:276 , LYS A:292 , ARG A:371 , TYR A:406 , HOH A:1087G , HOH A:1133E , HOH A:1384T , HOH A:1385T	BINDING SITE FOR RESIDUE SIA A 800
12	BC3	SOFTWARE	SER A:367 , SER A:370 , SER A:372 , ASN A:400 , THR A:401 , TRP A:403 , LYS A:432	BINDING SITE FOR RESIDUE SIA A 801
13	BC4	SOFTWARE	ASP A:293 , GLY A:297 , ASP A:324 , ASN A:347 , HOH A:1007W , HOH A:1089G	BINDING SITE FOR RESIDUE CA A 999
14	BC5	SOFTWARE	HOH A:1053W , HOH A:1305P	BINDING SITE FOR RESIDUE CA A 989

SS Bonds (9, 9)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

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

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:388
 aligned with NRAM_I75A5 | P03472 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:388
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462        
           NRAM_I75A5    83 RDFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTIRGKHSNGTIHDRSQYRALISWPLSSPPTVYNSRVECIGWSSTSCHDGKTRMSICISGPNNNASAVIWYNRRPVTEINTWARNILRTQESECVCHNGVCPVVFTDGSATGPAETRIYYFKEGKILKWEPLAGTAKHIEECSCYGERAEITCTCRDNWQGSNRPVIRIDPVAMTHTSQYICSPVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGVNTWLGRTISIASRSGYEMLKVPNALTDDKSKPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWTSNSIVSMCSSTEFLGQWDWPDGAKIEYFL 470
               SCOP domains d2qwba_ A: Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2qwbA00 A:82-468  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains Neur-2qwbA01 A:82-466                                                                                                                                                                                                                                                                                                                                                                             -- Pfam domains
         Sec.struct. author ..............eeeeeee..hhhhhhh.........eeee....eeeeeee.......hhh...........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee..............eee..eeeeeeeee.....eeeeeeeee..eeeeeee...........eeeee..eeeee..........eeeeee....eeeeee...........................................eeee.........eeeee.............eeeeee........eeee............eeeeeeeee.........eeeeeeeeeee..............hhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qwb A  82 RDFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTIRGKHSNGTIHDRSQYRALISWPLSSPPTVYNSRVECIGWSSTSCHDGKTRMSICISGPNNNASAVIWYNRRPVTEINTWARNILRTQESECVCHNGVCPVVFTDGSATGPAETRIYYFKEGKILKWEPLAGTAKHIEECSCYGERAEITCTCKDNWQGSNRPVIRIDPVAMTHTSQYICSPVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGVNTWLGRTISIASRSGYEMLKVPNALTDDKSKPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWTSNSIVSMCSSTEFLGQWDWPDGAKIEYFL 468
                                    91       101       111       121       131       141       151       161       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330  ||   341       351       361       371       381       391||     402       412|||    420       430       440       450       460        
                                                                                                                 169||                                                                                                                                                                333|                                                      392|               412|||                                                       
                                                                                                                  69A|                                                                                                                                                                 335                                                       394                12A||                                                       
                                                                                                                   170                                                                                                                                                                                                                                               12B|                                                       
                                                                                                                                                                                                                                                                                                                                                                      413

Legend:		→ Mismatch	(orange background)
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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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (15, 15)

Asymmetric Unit(hide GO term definitions)

Chain A (NRAM_I75A5 | P03472)

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.

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