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(-) Description

Title :  CRYSTAL STRUCTURE OF A SUBTYPE N11 NEURAMINIDASE-LIKE PROTEIN OF A/FLAT-FACED BAT/PERU/033/2010 (H18N11)
 
Authors :  X. Zhu, I. A. Wilson
Date :  11 Apr 13  (Deposition) - 23 Oct 13  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.68
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Influenza Virus, Neuraminidase-Like, N11, Beta Propeller, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Tong, X. Zhu, Y. Li, M. Shi, J. Zhang, M. Bourgeois, H. Yang, X. Chen, S. Recuenco, J. Gomez, L. M. Chen, A. Johnson, Y. Tao, C. Dreyfus, W. Yu, R. Mcbride, P. J. Carney, A. T. Gilbert, J. Chang, Z. Guo, C. T. Davis, J. C. Paulson, J. Stevens, C. E. Rupprecht, E. C. Holmes, I. A. Wilson, R. O. Donis
New World Bats Harbor Diverse Influenza A Viruses.
Plos Pathog. V. 9 03657 2013
PubMed-ID: 24130481  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1003657

(-) Compounds

Molecule 1 - NEURAMINIDASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PFASTBACHT-A
    Expression System Strain: HI5
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: ECTODOMAIN
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320
    Strain: A/FLAT-FACED BAT/PERU/033/2010(H18N11)

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 21)

Asymmetric/Biological Unit (5, 21)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2CA4Ligand/IonCALCIUM ION
3FUC1Ligand/IonALPHA-L-FUCOSE
4MAN1Ligand/IonALPHA-D-MANNOSE
5NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:293 , ASP A:297 , ASP A:324 , GLY A:345 , GLY A:347BINDING SITE FOR RESIDUE CA A 604
02AC2SOFTWAREASN B:293 , ASP B:297 , ASP B:324 , GLY B:345 , GLY B:347BINDING SITE FOR RESIDUE CA B 605
03AC3SOFTWAREASN C:293 , ASP C:297 , ASP C:324 , GLY C:345 , GLY C:347BINDING SITE FOR RESIDUE CA C 608
04AC4SOFTWAREASN D:293 , ASP D:297 , ASP D:324 , GLY D:345 , GLY D:347BINDING SITE FOR RESIDUE CA D 604
05AC5SOFTWAREALA A:82 , PHE A:187 , ASN A:259 , SER C:415BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 259 RESIDUES 601 TO 603
06AC6SOFTWAREALA B:82 , PHE B:187 , ASN B:259BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 259 RESIDUES 601 TO 602
07AC7SOFTWAREASN B:401 , ASN B:457 , HOH B:726 , SER D:150 , GLU D:151 , GLN D:152BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 401 RESIDUES 603 TO 604
08AC8SOFTWAREALA C:82 , VAL C:258 , ASN C:259 , SER D:415BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 259 RESIDUES 601 TO 602
09AC9SOFTWARESER A:150 , GLU A:151 , GLN A:152 , ASN C:401 , GLY C:459BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 401 RESIDUES 603 TO 607
10BC1SOFTWARESER B:415 , ASN D:259BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 259 RESIDUES 601 TO 603

(-) SS Bonds  (28, 28)

Asymmetric/Biological Unit
No.Residues
1A:92 -A:417
2A:124 -A:129
3A:183 -A:230
4A:232 -A:237
5A:280 -A:289
6A:318 -A:337
7A:421 -A:447
8B:92 -B:417
9B:124 -B:129
10B:183 -B:230
11B:232 -B:237
12B:280 -B:289
13B:318 -B:337
14B:421 -B:447
15C:92 -C:417
16C:124 -C:129
17C:183 -C:230
18C:232 -C:237
19C:280 -C:289
20C:318 -C:337
21C:421 -C:447
22D:92 -D:417
23D:124 -D:129
24D:183 -D:230
25D:232 -D:237
26D:280 -D:289
27D:318 -D:337
28D:421 -D:447

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Gly A:221 -Pro A:222
2Thr A:325 -Pro A:326
3Gly B:221 -Pro B:222
4Thr B:325 -Pro B:326
5Gly C:221 -Pro C:222
6Thr C:325 -Pro C:326
7Gly D:221 -Pro D:222
8Thr D:325 -Pro D:326

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K3Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K3Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4K3Y)

(-) Sequences/Alignments

Asymmetric/Biological 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:354
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4k3ya_ A: automated matches                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhh.........eeeeeee....eeeeeee........eeeeee.....hhhhheeeee..eeeeee....eeeeeee...eeeeee..eeeeee...............eee..eeeeeeee..hhhhheeeeeeee..eeeeeeee.......eeeeeeee..eeeeeee.........eeee.....eeee..................................ee...eeeeeeeee....eeeeeeeee...........eeeeeeeeeeeeeeeee............eeeeeeeee.....eeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4k3y A   82 ATPLVLGENLCSINGWVPTYRGEGTTGKIPDEQMLTRQNFVSCSDKECRRFFVSMGYVSEQMNVYSVKLGDPPTPDKLKFEAVGWSASSCHDGFQWTVLSVAGDGFVSILYGGIITDTIHPTNGGPLRTQASSCICNDGTCYTIIADGTTYTASSHRLYRLVNGTSAGWKALDTTGFNFEFPTCYYTSGKVKCTGTNLWNDAKRPFLEFDQSFTYTFKEPCLGFLGDTPRGIDTTNYCDKTTTEGEGGIQGFMIEGSNSWIGRIINPGSKKGFEIYKFLGTLFSVQTVGNRNYQLLSNSTIGRSGLYQPAYESRDCQELCFWIEIAATTKAGLSSNDLITFCGTGGSMPDVNWG  459
                                    91       101       111       121       131      |151||     164      |173       183       193  ||   206       216       226       236       246       256       266       276       286       296       306||     317       327  ||   340       350      |361       371       381   |||392A      |403       413|  |   421       431 ||    445       455    
                                                                                  138|  ||           170A                       196|                                                                                                        307|                  330| 337|               357|                       385|||  |    399|         413A  |               433|                     
                                                                                   149  ||                                       200                                                                                                         309                   333  339                359                        387||  |     401            415A                438                     
                                                                                      152|                                                                                                                                                                                                                             388|  |                                                                
                                                                                       156                                                                                                                                                                                                                              390  |                                                                
                                                                                                                                                                                                                                                                                                                          392A                                                                


Chain B from PDB  Type:PROTEIN  Length:354
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4k3yb_ B: automated matches                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeeeee...............eeeeeee....eeeeeee........eeeeee...........eeee..eeeeee....eeeeeee...eeeeee..eeeeee...............eee..eeeeeeee.......eeeeeeee..eeeeeeee.......eeeeeeee..eeeeeee.........eeee.....eeee..................................ee...eeeeeee......eeeeeeeee............eeeeeeeeeeeeeeee............eeeeeeeee.....eeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4k3y B   82 ATPLVLGENLCSINGWVPTYRGEGTTGKIPDEQMLTRQNFVSCSDKECRRFFVSMGYVSEQMNVYSVKLGDPPTPDKLKFEAVGWSASSCHDGFQWTVLSVAGDGFVSILYGGIITDTIHPTNGGPLRTQASSCICNDGTCYTIIADGTTYTASSHRLYRLVNGTSAGWKALDTTGFNFEFPTCYYTSGKVKCTGTNLWNDAKRPFLEFDQSFTYTFKEPCLGFLGDTPRGIDTTNYCDKTTTEGEGGIQGFMIEGSNSWIGRIINPGSKKGFEIYKFLGTLFSVQTVGNRNYQLLSNSTIGRSGLYQPAYESRDCQELCFWIEIAATTKAGLSSNDLITFCGTGGSMPDVNWG  459
                                    91       101       111       121       131      |151||     164      |173       183       193  ||   206       216       226       236       246       256       266       276       286       296       306||     317       327  ||   340       350      |361       371       381   |||392A      |403       413|  |   421       431 ||    445       455    
                                                                                  138|  ||           170A                       196|                                                                                                        307|                  330| 337|               357|                       385|||  |    399|         413A  |               433|                     
                                                                                   149  ||                                       200                                                                                                         309                   333  339                359                        387||  |     401            415A                438                     
                                                                                      152|                                                                                                                                                                                                                             388|  |                                                                
                                                                                       156                                                                                                                                                                                                                              390  |                                                                
                                                                                                                                                                                                                                                                                                                          392A                                                                


Chain C from PDB  Type:PROTEIN  Length:355
                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4k3yc_ C: automated matches                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhh........eeeeeeeee....eeeeeeeee.......eeeeee.....hhhhheeeee..eeeeee....eeeeeee...eeeeee..eeeeee...............eee..eeeeeeee..hhhhheeeeeeee..eeeeeeee.......eeeeeeee..eeeeeee.........eeee.....eeee..................................ee...eeeeeeeee....eeeeeeeee...........eeeeeeeeeeeeeeeee............eeeeeeeee.....eeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4k3y C   82 ATPLVLGENLCSINGWVPTYRGEGTTGKIPDEQMLTRQNFVSCSDKECRRFFVSMGYGVSEQMNVYSVKLGDPPTPDKLKFEAVGWSASSCHDGFQWTVLSVAGDGFVSILYGGIITDTIHPTNGGPLRTQASSCICNDGTCYTIIADGTTYTASSHRLYRLVNGTSAGWKALDTTGFNFEFPTCYYTSGKVKCTGTNLWNDAKRPFLEFDQSFTYTFKEPCLGFLGDTPRGIDTTNYCDKTTTEGEGGIQGFMIEGSNSWIGRIINPGSKKGFEIYKFLGTLFSVQTVGNRNYQLLSNSTIGRSGLYQPAYESRDCQELCFWIEIAATTKAGLSSNDLITFCGTGGSMPDVNWG  459
                                    91       101       111       121       131       150 ||    163       172       182       192   ||  205       215       225       235       245       255       265       275       285       295       305 ||    316       326   ||  339       349       360       370       380    |||392|      402       412 |  |  420       430  ||   444       454     
                                                                                   139|  ||           170A                       196|                                                                                                        307|                  330| 337|               357|                       385|||  |    399|         413A  |               433|                     
                                                                                    149  ||                                       200                                                                                                         309                   333  339                359                        387||  |     401            415A                438                     
                                                                                       152|                                                                                                                                                                                                                             388|  |                                                                
                                                                                        156                                                                                                                                                                                                                              390  |                                                                
                                                                                                                                                                                                                                                                                                                           392A                                                                


Chain D from PDB  Type:PROTEIN  Length:354
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4k3yd_ D: automated matches                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeeeee......ee.......eeeeeee....eeeeeee........eeeeee.....hhhhheeeee..eeeeee....eeeeeee...eeeeee..eeeeee...............eee..eeeeeeee.......eeeeeeee..eeeeeeee.......eeeeeeee..eeeeeee.........eeee.....eeee..................................ee....eeeeee......eeeeeeee.............eeeeeeeeeeeeeeee............eeeeeeeeee....eeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4k3y D   82 ATPLVLGENLCSINGWVPTYRGEGTTGKIPDEQMLTRQNFVSCSDKECRRFFVSMGYVSEQMNVYSVKLGDPPTPDKLKFEAVGWSASSCHDGFQWTVLSVAGDGFVSILYGGIITDTIHPTNGGPLRTQASSCICNDGTCYTIIADGTTYTASSHRLYRLVNGTSAGWKALDTTGFNFEFPTCYYTSGKVKCTGTNLWNDAKRPFLEFDQSFTYTFKEPCLGFLGDTPRGIDTTNYCDKTTTEGEGGIQGFMIEGSNSWIGRIINPGSKKGFEIYKFLGTLFSVQTVGNRNYQLLSNSTIGRSGLYQPAYESRDCQELCFWIEIAATTKAGLSSNDLITFCGTGGSMPDVNWG  459
                                    91       101       111       121       131      |151||     164      |173       183       193  ||   206       216       226       236       246       256       266       276       286       296       306||     317       327  ||   340       350      |361       371       381   |||392A      |403       413|  |   421       431 ||    445       455    
                                                                                  138|  ||           170A                       196|                                                                                                        307|                  330| 337|               357|                       385|||  |    399|         413A  |               433|                     
                                                                                   149  ||                                       200                                                                                                         309                   333  339                359                        387||  |     401            415A                438                     
                                                                                      152|                                                                                                                                                                                                                             388|  |                                                                
                                                                                       156                                                                                                                                                                                                                              390  |                                                                
                                                                                                                                                                                                                                                                                                                          392A
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K3Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K3Y)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4K3Y)

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 Related Entries

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4k3x