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(-) Description

Title :  N9 NEURAMINIDASE COMPLEXES WITH ANTIBODIES NC41 AND NC10: EMPIRICAL FREE-ENERGY CALCULATIONS CAPTURE SPECIFICITY TRENDS OBSERVED WITH MUTANT BINDING DATA
 
Authors :  W. R. Tulip, J. N. Varghese, P. M. Colman
Date :  06 May 94  (Deposition) - 15 Sep 95  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  H,L,N
Biol. Unit 1:  H,L,N  (4x)
Keywords :  Complex (Hydrolase-Immunoglobulin), Complex (Hydrolase- Immunoglobulin) Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. R. Tulip, V. R. Harley, R. G. Webster, J. Novotny
N9 Neuraminidase Complexes With Antibodies Nc41 And Nc10: Empirical Free Energy Calculations Capture Specificity Trends Observed With Mutant Binding Data.
Biochemistry V. 33 7986 1994
PubMed-ID: 7517697  |  Reference-DOI: 10.1021/BI00192A002
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - N9 NEURAMINIDASE
    Chains: N
    EC Number: 3.2.1.18
    Mutation: YES
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320
 
Molecule 2 - FAB NC10
    Chains: L
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: RESOLUTION OF 3.0 ANGSTROMS
    Other Details - Source: ISOLATED FROM MONOCLONAL MURINE ANTIBODY
 
Molecule 3 - FAB NC10
    Chains: H
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: RESOLUTION OF 3.0 ANGSTROMS
    Other Details - Source: ISOLATED FROM MONOCLONAL MURINE ANTIBODY

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : HLN
Biological Unit 1 (4x): HLN

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN3Ligand/IonALPHA-D-MANNOSE
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 28)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2MAN12Ligand/IonALPHA-D-MANNOSE
3NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN N:200 , LEU N:453 , GLY N:454 , GLN N:455 , NAG N:470BBINDING SITE FOR RESIDUE NAG N 469A
2AC2SOFTWAREGLN N:392 , GLY N:394 , NAG N:469A , BMA N:471CBINDING SITE FOR RESIDUE NAG N 470B
3AC3SOFTWARELEU N:377 , PRO N:390 , GLY N:394 , NAG N:470B , MAN N:472DBINDING SITE FOR RESIDUE BMA N 471C
4AC4SOFTWAREARG N:364 , GLU N:375 , BMA N:471C , MAN N:473E , MAN N:474FBINDING SITE FOR RESIDUE MAN N 472D
5AC5SOFTWAREARG H:100 , ASP N:330 , ARG N:389 , MAN N:472D , MAN N:474FBINDING SITE FOR RESIDUE MAN N 473E
6AC6SOFTWAREARG H:100 , ASP H:100B , ARG N:327 , ASN N:329 , ASP N:330 , ARG N:364 , ILE N:366 , MAN N:472D , MAN N:473EBINDING SITE FOR RESIDUE MAN N 474F
7AC7SOFTWAREPHE N:84 , ASN N:86 , ASN N:234BINDING SITE FOR RESIDUE NAG N 475A

(-) SS Bonds  (11, 11)

Asymmetric Unit
No.Residues
1H:22 -H:92
2L:23 -L:88
3N:92 -N:417
4N:124 -N:129
5N:175 -N:193
6N:183 -N:230
7N:232 -N:237
8N:278 -N:291
9N:280 -N:289
10N:318 -N:337
11N:421 -N:447

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asn N:325 -Pro N:326
2Arg N:430 -Pro N:431
3Leu L:94 -Pro L:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NMA)

(-) 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 H from PDB  Type:PROTEIN  Length:122
                                                                                                                                                           
               SCOP domains d1nmah_ H: Immunoglobulin heavy chain variable domain, VH                                                                  SCOP domains
               CATH domains 1nmaH00 H:1-113 Immunoglobulins                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeeee...eeeeeeeee...hhh.eeeeeeee.....eeeeeee....eeee...hhh.eeeeeehhh.eeeeeee...hhh.eeeeeeee.........eeee....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                1nma H    1 EVQLQQPGAELVKPGASVRMSCKASGYTFTNYNMYWVKQSPGQGLEWIGIFYPGNGDTSYNQKFKDKATLTADKSSNTAYMQLSSLTSEDSAVYYCARSGGSYRYDGGFDYWGQGTTLTVSS  113
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111  
                                                                              52A                            82A||               100A||||             
                                                                                                              82B|                100B|||             
                                                                                                               82C                 100C||             
                                                                                                                                    100D|             
                                                                                                                                     100E             


Chain L from PDB  Type:PROTEIN  Length:109
                                                                                                                                              
               SCOP domains d1nmal_ L: Immunoglobulin light chain kappa variable domain, VL-kappa                                         SCOP domains
               CATH domains 1nmaL00 L:1-109 Immunoglobulins                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee............eeeeeee.......eeeeee.....eeeee.............eeeeee..eeeeee....hhh..eeeeee................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                1nma L    1 DIQMTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQNPDGTVKLLIYYTSNLHSEVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQDFTLPFTFGGGTKLEIRRA  109
                                    10        20        30        40        50        60        70        80        90       100         


Chain N from PDB  Type:PROTEIN  Length:378
 aligned with NRAM_I84A1 | P05803 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:378
                                    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        
          NRAM_I84A1     83 REFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTIRGKHSNGTIHDRSQYRDLISWPLSSPPTVYNSRVECIGWSSTSCHDGRARMSICISGPNNNASAVIWYNRRPVTEINTWARNILRTQESECVCQNGVCPVVFTDGSATGPAETRIYYFKEGKILKWEPLTGTAKHIEECSCYGEQAGVTCTCRDNWQGSNRPVIQIDPVAMTHTSQYICSPVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGGNTWLGRTISIASRSGYEMLKVPNALTDDRSKPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWTSNSIVSMCSSTEFLGQWNW  460
               SCOP domains d1nman_ N: Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1nmaN00 N:82-458  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains Neur-1nmaN01 N:82-458                                                                                                                                                                                                                                                                                                                                                                      Pfam domains
         Sec.struct. author ..............eeeeeeee.hhhhhhh.....eeeeeeeee..eeeeeeee.......hhh...........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee..............eee..eeeeeeeee.....eeeeeeeee..eeeeeee...........eeee....eeee..........eeeeee....eeeeee...................................eeee..eeeeee.........eeeee.............eeeeee........eeeee..........eeeeeeeeee.........eeeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1nma N   82 REFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTIRGKHSNGTIHDRSQYRDLISWPLSSPPTVYNSRVECIGWSSTSCHDGRARMSICISGPNNNASAVIWYNRRPVTEINTWARNILRTQESECVCQNGVCPVVFTDGSATGPAETRIYYFKEGKILKWEPLTGTAKHIEECSCYGEQAGVTCTCRDNWQGSNRPVIQIDPVAMTHTSQYICSPVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGGNTWLGRTISIASRSGYEMLKVPNALTDDKSRPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWTSNSIVSMCSSTEFLGQWNW  458
                                    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        
                                                                                                                 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  (3, 3)

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

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Sialidase (56)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain N   (NRAM_I84A1 | P05803)
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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  3.2.1.18
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 Related Entries

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

UniProtKB/Swiss-Prot
        NRAM_I84A1 | P05803: 1ncd 1nmb 2b8h

(-) Related Entries Specified in the PDB File

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