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(-) Description

Title :  STRUCTURES OF AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE
 
Authors :  M. J. Jedrzejas, M. Luo
Date :  12 Dec 94  (Deposition) - 31 Mar 95  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Hydrolase (O-Glycosyl) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Jedrzejas, S. Singh, W. J. Brouillette, W. G. Laver, G. M. Air, M. Luo
Structures Of Aromatic Inhibitors Of Influenza Virus Neuraminidase.
Biochemistry V. 34 3144 1995
PubMed-ID: 7880809  |  Reference-DOI: 10.1021/BI00010A003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INFLUENZA A SUBTYPE N2 NEURAMINIDASE
    Chains: A, B
    EC Number: 3.2.1.18
    Engineered: YES
    Organism Scientific: INFLUENZA A VIRUS (STRAIN A/TOKYO/3/1967 H2N2)
    Organism Taxid: 380960
    Strain: A/TOKYO/3/1967 H2N2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 32)

Asymmetric Unit (7, 32)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2CA2Ligand/IonCALCIUM ION
3DAN2Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
4FUC1Ligand/IonALPHA-L-FUCOSE
5FUL1Ligand/IonBETA-L-FUCOSE
6MAN6Ligand/IonALPHA-D-MANNOSE
7NAG16Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (6, 60)
No.NameCountTypeFull Name
1BMA8Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3DAN4Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
4FUC2Ligand/IonALPHA-L-FUCOSE
5FUL2Ligand/IonBETA-L-FUCOSE
6MAN12Ligand/IonALPHA-D-MANNOSE
7NAG32Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (34, 34)

Asymmetric Unit (34, 34)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:83 , ASN A:86 , SER A:88 , NAG A:473 , NAG A:485BINDING SITE FOR RESIDUE NAG A 472
02AC2SOFTWARENAG A:472BINDING SITE FOR RESIDUE NAG A 473
03AC3SOFTWAREASN A:146 , TRP A:437 , NAG A:475 , FUL A:477BINDING SITE FOR RESIDUE NAG A 474
04AC4SOFTWARENAG A:474 , BMA A:476BINDING SITE FOR RESIDUE NAG A 475
05AC5SOFTWARENAG A:475BINDING SITE FOR RESIDUE BMA A 476
06AC6SOFTWARENAG A:474 , ASN B:463 , PHE B:466BINDING SITE FOR RESIDUE FUL A 477
07AC7SOFTWAREASN A:200 , TYR B:453 , GLY B:454 , THR B:455 , NAG B:479 , MAN B:483 , HOH B:512BINDING SITE FOR RESIDUE NAG B 478
08AC8SOFTWAREASN B:393 , ARG B:394 , TYR B:453 , NAG B:478 , BMA B:480 , MAN B:483BINDING SITE FOR RESIDUE NAG B 479
09AC9SOFTWAREGLN B:391 , ILE B:392 , ARG B:394 , NAG B:479 , MAN B:481BINDING SITE FOR RESIDUE BMA B 480
10BC1SOFTWAREGLN B:391 , BMA B:480 , MAN B:482BINDING SITE FOR RESIDUE MAN B 481
11BC2SOFTWAREARG B:394 , MAN B:481BINDING SITE FOR RESIDUE MAN B 482
12BC3SOFTWARENAG B:478 , NAG B:479BINDING SITE FOR RESIDUE MAN B 483
13BC4SOFTWAREASN A:234 , TYR A:284 , GLU A:308 , NAG A:485BINDING SITE FOR RESIDUE NAG A 484
14BC5SOFTWARENAG A:472 , NAG A:484BINDING SITE FOR RESIDUE NAG A 485
15BC6SOFTWAREGLU B:83 , ASN B:86 , SER B:88 , NAG B:473 , NAG B:491BINDING SITE FOR RESIDUE NAG B 472
16BC7SOFTWARENAG B:472BINDING SITE FOR RESIDUE NAG B 473
17BC8SOFTWAREASN B:146 , TRP B:437 , NAG B:475 , FUC B:477BINDING SITE FOR RESIDUE NAG B 474
18BC9SOFTWAREARG B:331 , NAG B:474 , BMA B:476BINDING SITE FOR RESIDUE NAG B 475
19CATAUTHORARG A:118 , GLU A:119 , ASP A:151 , ARG A:152 , TRP A:178 , ILE A:222 , ARG A:224 , GLU A:276 , ARG A:292 , ARG A:371 , TYR A:406SUBSTRATE (SIALIC ACID) BINDING RESIDUES IN CATALYTIC SITE
20CC1SOFTWAREARG B:331 , NAG B:475BINDING SITE FOR RESIDUE BMA B 476
21CC2SOFTWAREASN A:463 , PHE A:466 , NAG B:474BINDING SITE FOR RESIDUE FUC B 477
22CC3SOFTWARETYR A:453 , GLY A:454 , THR A:455 , ASN B:200 , NAG B:485 , MAN B:489BINDING SITE FOR RESIDUE NAG B 484
23CC4SOFTWAREASN A:393 , ARG A:394 , TYR A:453 , NAG B:484 , BMA B:486 , MAN B:489BINDING SITE FOR RESIDUE NAG B 485
24CC5SOFTWAREGLN A:391 , ILE A:392 , ARG A:394 , NAG B:485 , MAN B:487BINDING SITE FOR RESIDUE BMA B 486
25CC6SOFTWAREGLN A:391 , HOH A:542 , BMA B:486 , MAN B:488BINDING SITE FOR RESIDUE MAN B 487
26CC7SOFTWAREARG A:394 , MAN B:487BINDING SITE FOR RESIDUE MAN B 488
27CC8SOFTWARENAG B:484 , NAG B:485BINDING SITE FOR RESIDUE MAN B 489
28CC9SOFTWAREASN B:234 , TYR B:284 , GLU B:308 , NAG B:491BINDING SITE FOR RESIDUE NAG B 490
29CT2UNKNOWNARG B:118 , GLU B:119 , ASP B:151 , ARG B:152 , TRP B:178 , ILE B:222 , ARG B:224 , GLU B:276 , ARG B:292 , ARG B:371 , TYR B:406NULL
30DC1SOFTWARENAG B:472 , NAG B:490BINDING SITE FOR RESIDUE NAG B 491
31DC2SOFTWAREASP A:293 , GLY A:297 , ASP A:324 , GLY A:345 , GLN A:347 , HOH A:592BINDING SITE FOR RESIDUE CA A 470
32DC3SOFTWAREASP B:293 , GLY B:297 , ASP B:324 , GLY B:345 , GLN B:347BINDING SITE FOR RESIDUE CA B 470
33DC4SOFTWAREARG A:118 , GLU A:119 , ASP A:151 , ARG A:152 , ARG A:224 , ALA A:246 , GLU A:276 , ASN A:294 , ARG A:371 , TYR A:406 , HOH A:496 , HOH A:564 , HOH A:594BINDING SITE FOR RESIDUE DAN A 471
34DC5SOFTWAREARG B:118 , GLU B:119 , ASP B:151 , ARG B:152 , ARG B:224 , ALA B:246 , GLU B:276 , ASN B:294 , ARG B:371 , TYR B:406BINDING SITE FOR RESIDUE DAN B 471

(-) SS Bonds  (18, 18)

Asymmetric Unit
No.Residues
1A:92 -A:417
2A:124 -A:129
3A:175 -A:193
4A:183 -A:230
5A:232 -A:237
6A:278 -A:291
7A:280 -A:289
8A:318 -A:337
9A:421 -A:447
10B:92 -B:417
11B:124 -B:129
12B:175 -B:193
13B:183 -B:230
14B:232 -B:237
15B:278 -B:291
16B:280 -B:289
17B:318 -B:337
18B:421 -B:447

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:284 -Pro A:285
2Thr A:325 -Pro A:326
3Tyr B:284 -Pro B:285
4Thr B:325 -Pro B:326

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IVF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IVF)

(-) Exons   (0, 0)

(no "Exon" information available for 1IVF)

(-) Sequences/Alignments

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:388
 aligned with NRAM_I67A0 | P06820 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:388
                                    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        
           NRAM_I67A0    82 VEYRNWSKPQCQITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPVKCYQFALGQGTTLDNKHSNDTVHDRIPHRTLLMNELGVPFHLGTRQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYDGRLVDSIGSWSQNILRTQESECVCINGTCTVVMTDGSASGRADTRILFIEEGKIVHISPLAGSAQHVEECSCYPRYPGVRCICRDNWKGSNRPVVDINMEDYSIDSSYVCSGLVGDTPRNDDRSSNSNCRNPNNERGTQGVKGWAFDNGNDLWMGRTISKDLRSGYETFKVIGGWSTPNSKSQINRQVIVDSDNRSGYSGIFSVEGKSCINRCFYVELIRGRKQETRVWWTSNSIVVFCGTSGTYGTGSWPDGANINFMPI 469
               SCOP domains d1ivfa_ A: Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1ivfA00 A:82-469  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee..hhhhhhh.....eeeeeeee....eeeeeee.......hhh...........eeeeee.........eeeee..eeeeee....eeeeeeee....eeeeeee..eeeeeee..............eee..eeeeeeeee.....eeeeeeeee..eeeeeee...........eeeee..eeeee..........eeeeee.....eeeee....................................eeee..eeeeee.........eeeeeee.........eee..eeee........eeeeeee....eeeeeee.eeee.........eeee.eeeeee.................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ivf A  82 VEYRNWSKPQCQITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPVKCYQFALGQGTTLDNKHSNDTVHDRIPHRTLLMNELGVPFHLGTRQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYDGRLVDSIGSWSQNILRTQESECVCINGTCTVVMTDGSASGRADTRILFIEEGKIVHISPLAGSAQHVEECSCYPRYPGVRCICRDNWKGSNRPVVDINMEDYSIDSSYVCSGLVGDTPRNDDRSSNSNCRDPNNERGTQGVKGWAFDNGNDLWMGRTISKDLRSGYETFKVIGGWSTPNSKSQINRQVIVDSDNRSGYSGIFSVEGKSCINRCFYVELIRGRKQETRVWWTSNSIVVFCGTSGTYGTGSWPDGANINFMPI 469
                                    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        


Chain B from PDB  Type:PROTEIN  Length:388
 aligned with NRAM_I67A0 | P06820 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:388
                                    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        
           NRAM_I67A0    82 VEYRNWSKPQCQITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPVKCYQFALGQGTTLDNKHSNDTVHDRIPHRTLLMNELGVPFHLGTRQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYDGRLVDSIGSWSQNILRTQESECVCINGTCTVVMTDGSASGRADTRILFIEEGKIVHISPLAGSAQHVEECSCYPRYPGVRCICRDNWKGSNRPVVDINMEDYSIDSSYVCSGLVGDTPRNDDRSSNSNCRNPNNERGTQGVKGWAFDNGNDLWMGRTISKDLRSGYETFKVIGGWSTPNSKSQINRQVIVDSDNRSGYSGIFSVEGKSCINRCFYVELIRGRKQETRVWWTSNSIVVFCGTSGTYGTGSWPDGANINFMPI 469
               SCOP domains d1ivfb_ B: Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1ivfB00 B:82-469  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee..hhhhhhh.....eeeeeeee....eeeeeee.......hhh...........eeeeee.........eeeee..eeeeee....eeeeeeee....eeeeeee..eeeeeee..............eee..eeeeeeeee.....eeeeeeeee..eeeeeee...........eeeee..eeeee..........eeeeee.....eeeee....................................eeee..eeeeee.........eeeeeee.........eee..eeee........eeeeeee....eeeeeee.eeee.........eeee.eeeeee.................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ivf B  82 VEYRNWSKPQCQITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPVKCYQFALGQGTTLDNKHSNDTVHDRIPHRTLLMNELGVPFHLGTRQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYDGRLVDSIGSWSQNILRTQESECVCINGTCTVVMTDGSASGRADTRILFIEEGKIVHISPLAGSAQHVEECSCYPRYPGVRCICRDNWKGSNRPVVDINMEDYSIDSSYVCSGLVGDTPRNDDRSSNSNCRDPNNERGTQGVKGWAFDNGNDLWMGRTISKDLRSGYETFKVIGGWSTPNSKSQINRQVIVDSDNRSGYSGIFSVEGKSCINRCFYVELIRGRKQETRVWWTSNSIVVFCGTSGTYGTGSWPDGANINFMPI 469
                                    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
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IVF)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NRAM_I67A0 | P06820)
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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NRAM_I67A0 | P06820: 1ing 1inh 1inw 1inx 1ivc 1ivd 1ive 1ivg 1nn2 2bat

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1IVF)