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(-) Description

Title :  STRUCTURE OF NEURAMINIDASE SUBTYPE N9 COMPLEXED WITH 30 MM SIALIC ACID (NANA, NEU5AC), CRYSTAL SOAKED FOR 24 HOURS AT 291 K AND FINALLY BACKSOAKED FOR 30 MIN IN A CRYOPROTECTANT SOLUTION WHICH DID NOT CONTAIN NEU5AC
 
Authors :  E. Rudino-Pinera, P. Tunnah, S. J. Crennell, R. G. Webster, W. G. Laver, E. F. Garman
Date :  20 Oct 05  (Deposition) - 27 Mar 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Hydrolase, Influenza Type A, Neuraminidase, Sialic Acid, Subtype N9, Glycoprotein, Glycosidase, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Rudino-Pinera, S. J. Crennell, R. G. Webster, W. G. Laver, E. F. Garman
The Crystal Structure Of Influenza Type A Virus Neuraminidase Of The N6 Subtype At 1. 85 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NEURAMINIDASE SUBTYPE N9
    Chains: A
    EC Number: 3.2.1.18
    Engineered: YES
    Expression System: GALLUS GALLUS
    Expression System Taxid: 9031
    Fragment: RESIDUES 83-470
    Organism Common: AVIAN INFLUENZA VIRUS A
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320
    Strain: A/TERN/STERNA ALBIFRONS/N9

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric Unit (5, 15)
No.NameCountTypeFull Name
1BMA5Ligand/IonBETA-D-MANNOSE
2CA1Ligand/IonCALCIUM ION
3MAN2Ligand/IonALPHA-D-MANNOSE
4NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SIA2Ligand/IonO-SIALIC ACID
Biological Unit 1 (4, 56)
No.NameCountTypeFull Name
1BMA20Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3MAN8Ligand/IonALPHA-D-MANNOSE
4NAG20Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SIA8Ligand/IonO-SIALIC ACID

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:118 , GLU A:119 , ASP A:151 , ARG A:152 , ARG A:224 , ALA A:246 , GLU A:276 , GLU A:277 , ARG A:292 , ARG A:371 , TYR A:406 , HOH A:2057 , HOH A:2081 , HOH A:2223 , HOH A:2224 , HOH A:2225BINDING SITE FOR RESIDUE SIA A1469
02AC2SOFTWARESER A:367 , SER A:370 , SER A:372 , ASN A:400 , THR A:401 , ASP A:402 , TRP A:403 , LYS A:432BINDING SITE FOR RESIDUE SIA A1470
03AC3SOFTWAREASN A:199 , ASN A:200 , LEU A:453 , GLY A:454 , GLN A:455 , NAG A:1472 , HOH A:2211 , HOH A:2226 , HOH A:2227BINDING SITE FOR RESIDUE NAG A1471
04AC4SOFTWAREGLN A:392 , GLY A:394 , NAG A:1471 , BMA A:1476 , HOH A:2173 , HOH A:2226 , HOH A:2229BINDING SITE FOR RESIDUE NAG A1472
05AC5SOFTWAREASP A:83 , PHE A:84 , ASN A:86 , ASN A:234 , NAG A:1474 , HOH A:2228BINDING SITE FOR RESIDUE NAG A1473
06AC6SOFTWAREASP A:83 , NAG A:1473BINDING SITE FOR RESIDUE NAG A1474
07AC7SOFTWAREASN A:146 , TRP A:437BINDING SITE FOR RESIDUE NAG A1475
08AC8SOFTWARELEU A:377 , THR A:391 , GLN A:392 , GLY A:394 , NAG A:1472 , MAN A:1477 , BMA A:1480 , HOH A:2165 , HOH A:2170 , HOH A:2229BINDING SITE FOR RESIDUE BMA A1476
09AC9SOFTWAREARG A:364 , GLU A:375 , BMA A:1476 , MAN A:1478 , BMA A:1479 , HOH A:2230BINDING SITE FOR RESIDUE MAN A1477
10BC1SOFTWAREASP A:330 , ARG A:364 , LYS A:389 , PRO A:390 , MAN A:1477 , BMA A:1479 , HOH A:2232BINDING SITE FOR RESIDUE MAN A1478
11BC2SOFTWAREARG A:327 , ASN A:329 , ASP A:330 , ARG A:364 , ILE A:366 , ILE A:368 , MAN A:1477 , MAN A:1478 , HOH A:2140 , HOH A:2233BINDING SITE FOR RESIDUE BMA A1479
12BC3SOFTWAREBMA A:1476 , BMA A:1481 , BMA A:1482BINDING SITE FOR RESIDUE BMA A1480
13BC4SOFTWAREBMA A:1480BINDING SITE FOR RESIDUE BMA A1481
14BC5SOFTWAREBMA A:1480 , HOH A:2229BINDING SITE FOR RESIDUE BMA A1482
15BC6SOFTWAREASP A:293 , GLY A:297 , ASP A:324 , ASN A:347 , HOH A:2138 , HOH A:2145BINDING SITE FOR RESIDUE CA A1483

(-) SS Bonds  (9, 9)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:325 -Pro A:326
2Arg A:430 -Pro A:431

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C4L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2C4L)

(-) Exons   (0, 0)

(no "Exon" information available for 2C4L)

(-) 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_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 d2c4la_ A: Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2c4lA00 A:82-468  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhhh....eeeeeeeeeee..eeeeeeeeeeee..hhhhh..........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee...................eeeeeeeee.....eeeeeeeee..eeeeeee........eeeeeeee..eeeeeee........eeeeee....eeeeee...................................ee......eeee.......eeeeeee.............eeeeeeeeeee...eeee............eeeeeeeee.........eeeeeeeeeee.............hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2c4l A   82 RDFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTIRGKHSNGTIHDRSQYRALISWPLSSPPTVYNSRVECIGWSSTSCHDGKTRMSICISGPNNNASAVIWYNRRPVTEINTWARNILRTQESECVCHNGVCPVVFTDGSATGPAETRIYYFKEGKILKWEPLAGTAKHIEECSCYGERAEITCTCRDNWQGSNRPVIRIDPVAMTHTSQYICSPVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGVNTWLGRTISIASRSGYEMLKVPNALTDDKSKPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWTSNSIVSMCSSTEFLGQWDWPDGAKIEYFL  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        
                                                                                                                 169A                                                                                                                                                                 333|                                                      392|               412A|                                                        
                                                                                                                                                                                                                                                                                       335                                                       394                412B
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C4L)

(-) 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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  2c4l
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  NRAM_I75A5 | P03472
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  3.2.1.18
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 Related Entries

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

UniProtKB/Swiss-Prot
        NRAM_I75A5 | P03472: 1a14 1bji 1f8b 1f8c 1f8d 1f8e 1iny 1l7f 1l7g 1l7h 1mwe 1nca 1ncb 1ncc 1nmc 1nna 1nnb 1nnc 1xoe 1xog 2c4a 2qwa 2qwb 2qwc 2qwd 2qwe 2qwf 2qwg 2qwh 2qwi 2qwj 2qwk 3nn9 3w09 4dgr 4nn9 4weg 5nn9 6nn9 7nn9

(-) Related Entries Specified in the PDB File

1a14 COMPLEX BETWEEN NC10 ANTI-INFLUENZA VIRUS NEURAMINIDASE SINGLE CHAIN ANTIBODY WITH A 5 RESIDUE LINKER AND INFLUENZA VIRUS NEURAMINIDASE
1bji THE X-RAY STRUCTURE OF A COMPLEX OF TERN N9 INFLUENZA VIRUS NEURAMINIDASE COMPLEXED WITH THE GLAXO 6-CARBOXAMIDE SIALIC ACID ANALOGUE GR217029
1f8b NATIVE INFLUENZA VIRUS NEURAMINIDASE IN COMPLEX WITHNEU5AC2EN
1f8c NATIVE INFLUENZA NEURAMINIDASE IN COMPLEX WITH 4-AMINO-2-DEOXY-2,3-DEHYDRO-N- NEURAMINIC ACID
1f8d NATIVE INFLUENZA NEURAMINIDASE IN COMPLEX WITH 9-AMINO-2-DEOXY-2,3-DEHYDRO-N- NEURAMINIC ACID
1f8e NATIVE INFLUENZA NEURAMINIDASE IN COMPLEX WITH 4,9-DIAMINO-2-DEOXY-2,3-DEHYDRO-N- ACETYL-NEURAMINIC ACID
1iny INFLUENZA A SUBTYPE N9 NEURAMINIDASE (SIALIDASE) COMPLEXED WITH EPANA INHIBITOR (4- ACETAMIDO- 2,4-DIDEOXY-D-GLYCERO-ALPHA-D- GALACTO-1-OCTOPYRANOSYL) PHOSPHONIC ACID
1l7f CRYSTAL STRUCTURE OF INFLUENZA VIRUS NEURAMINIDASE INCOMPLEX WITH BCX-1812
1l7g CRYSTAL STRUCTURE OF E119G MUTANT INFLUENZA VIRUSNEURAMINIDASE IN COMPLEX WITH BCX-1812
1l7h CRYSTAL STRUCTURE OF R292K MUTANT INFLUENZA VIRUSNEURAMINIDASE IN COMPLEX WITH BCX-1812
1mwe THE X-RAY STRUCTURE OF A COMPLEX OF TERN N9 INFLUENZA VIRUS NEURAMINIDASE COMPLEXED WITH SIALIC ACID AT 4 DEGREES C REVEALING A SECOND SIALIC ACID BINDING SITE
1nca N9 NEURAMINIDASE-NC41 COMPLEX WITH FAB
1ncb N9 NEURAMINIDASE-NC41 MUTANT WITH ASN 329 REPLACED BY ASP (N329D) COMPLEX WITH FAB
1ncc N9 NEURAMINIDASE-NC41 MUTANT WITH ILE 368 REPLACED BY ARG (I368R) COMPLEX WITH FAB
1nmc COMPLEX BETWEEN NC10 ANTI-INFLUENZA VIRUS NEURAMINIDASE SINGLE CHAIN ANTIBODY WITH A 15 RESIDUE LINKER AND INFLUENZA VIRUS NEURAMINIDASE
1nna NEURAMINIDASE (SIALIDASE)
1nnb NEURAMINIDASE (SIALIDASE) COMPLEXED WITH 2- DEOXY-2,3-DEHYDRO-N-ACETYL NEURAMINIC ACID
1nnc INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) COMPLEXED WITH 4-GUANIDINO-NEU5AC2EN INHIBITOR
1xoe N9 TERN INFLUENZA NEURAMINIDASE COMPLEXED WITH (2R,4R,5R)-5-(1-ACETYLAMINO-3-METHYL- BUTYL-PYRROLIDINE-2, 4-DICAROBYXYLIC ACID 4 -METHYL ESTERDASE COMPLEXED WITH
1xog N9 TERN INFLUENZA NEURAMINIDASE COMPLEXED WITH A 2,5-DISUBSTITUTED TETRAHYDROFURAN-5- CARBOXYLIC ACID
2c4a STRUCTURE OF NEURAMINIDASE SUBTYPE N9 COMPLEXED WITH 30 MM SIALIC ACID (NANA, NEU5AC), CRYSTAL SOAKED FOR 3 HOURS AT 291 K.
2qwa THE X-RAY STRUCTURE OF A DRUG RESISTANT VARIANT R292K OF TERN N9 INFLUENZA VIRUS NEURAMINIDASE
2qwb THE X-RAY STRUCTURE OF A COMPLEX OF SIALIC ACID AND A DRUG RESISTANT VARIANT R292K OF TERN N9 INFLUENZA VIRUS NEURAMINIDASE
2qwc THE X-RAY STRUCTURE OF A COMPLEX OF NEU5AC2EN AND A DRUG RESISTANT VARIANT R292K OF TERN N9 INFLUENZA VIRUS NEURAMINIDASE
2qwd THE X-RAY STRUCTURE OF A COMPLEX OF 4- AMINO-NEU5AC2EN AND A DRUG RESISTANT VARIANT R292K OF TERN N9 INFLUENZA VIRUS NEURAMINIDASE
2qwe THE X-RAY STRUCTURE OF A COMPLEX OF 4- GUANIDINO-NEU5AC2EN AND A DRUG RESISTANT VARIANT R292K OF TERN N9 INFLUENZA VIRUS NEURAMINIDASE
2qwf THE X-RAY STRUCTURE OF A COMPLEX OF N- ACETYL-4-GUANIDINO-6- METHYL(PROPYL) CARBOXAMIDE-4,5-DIHYDRO-2H-PYRAN-2- CARBOXYLIC ACID AND A DRUG RESISTANT VARIANT R292K OF TERN N9 INFLUENZA VIRUS NEURAMINIDASE
2qwg THE X-RAY STRUCTURE OF A COMPLEX OF 5- N-ACETYL-4-AMINO-6- DIETHYLCARBOXAMIDE-4,5 -DIHYDRO-2H-PYRAN-2-CARBOXYLIC ACID AND A DRUG RESISTANT VARIANT R292K OF TERN N9 INFLUENZA VIRUS NEURAMINIDASE
2qwh THE X-RAY STRUCTURE OF A COMPLEX OF 5- N-ACETYL-5-AMINO-3- (1-ETHYLPROPOXY)-1- CYCLOHEXENE-1-CARBOXYLIC ACID (GS4071) AND A DRUG RESISTANT VARIANT R292K OF TERN N9 INFLUENZA VIRUS NEURAMINIDASE
2qwi THE X-RAY STRUCTURE OF A COMPLEX OF N- ACETYL-4-GUANIDINO-6- METHYL(PROPYL) CARBOXAMIDE-4,5-DIHYDRO-2H-PYRAN-2- CARBOXYLIC ACID AND WILDTYPE TERN N9 INFLUENZA VIRUS NEURAMINIDASE
2qwj THE X-RAY STRUCTURE OF A COMPLEX OF 5- N-ACETYL-4-AMINO-6- DIETHYLCARBOXAMIDE-4,5 -DIHYDRO-2H-PYRAN-2-CARBOXYLIC ACID AND A DRUG RESISTANT VARIANT R292K OF TERN N9 INFLUENZA VIRUS NEURAMINIDASE
2qwk THE X-RAY STRUCTURE OF A COMPLEX OF 5- N-ACETYL-5-AMINO-3- (1-ETHYLPROPOXY)-1- CYCLOHEXENE-1-CARBOXYLIC ACID (GS4071) AND WILDTYPE TERN N9 INFLUENZA VIRUS NEURAMINIDASE
3nn9 NEURAMINIDASE N9 (SIALIDASE) (MUTANT WITH ASN 329 REPLACED BY ASP) (N329D)
4nn9 NEURAMINIDASE N9 (SIALIDASE) (MUTANT WITH ILE 368 REPLACED BY ARG) (I368R)
5nn9 NEURAMINIDASE N9 (SIALIDASE) (MUTANT WITH ALA 369 REPLACED BY ASP) (A369D)
6nn9 NEURAMINIDASE N9 (SIALIDASE) (MUTANT WITH LYS 432 REPLACED BY ASN) (K432N)
7nn9 NATIVE INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN)