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(-) Description

Title :  CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NANC, COMPLEX WITH NEU5AC AND NEU5AC2EN FOLLOWING SOAKING WITH 3'SL
 
Authors :  C. D. Owen, P. Lukacik, J. A. Potter, M. Walsh, G. L. Taylor
Date :  20 Mar 15  (Deposition) - 23 Sep 15  (Release) - 25 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Sialidase, Cbm40, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. D. Owen, P. Lukacik, J. A. Potter, O. Sleator, G. L. Taylor, M. A. Wals
Streptococcus Pneumoniae Nanc: Structural Insights Into The Specificity And Mechanism Of A Sialidase That Produces A Sialidase Inhibitor.
J. Biol. Chem. V. 290 27736 2015
PubMed-ID: 26370075  |  Reference-DOI: 10.1074/JBC.M115.673632

(-) Compounds

Molecule 1 - NEURAMINIDASE C
    Chains: A, B
    EC Number: 3.2.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NANC, SPG_1219
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Strain: G54

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric Unit (5, 7)
No.NameCountTypeFull Name
1DAN1Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
2GOL1Ligand/IonGLYCEROL
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PO41Ligand/IonPHOSPHATE ION
5SIA2Ligand/IonO-SIALIC ACID
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1DAN-1Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
2GOL-1Ligand/IonGLYCEROL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PO41Ligand/IonPHOSPHATE ION
5SIA1Ligand/IonO-SIALIC ACID
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
1DAN1Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
2GOL1Ligand/IonGLYCEROL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PO4-1Ligand/IonPHOSPHATE ION
5SIA1Ligand/IonO-SIALIC ACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:128 , PHE A:149 , ARG A:151 , GLU A:159 , ARG A:161 , ARG A:237 , PHE A:243 , HOH A:934 , HOH A:1079binding site for residue SIA A 801
2AC2SOFTWAREARG A:290 , ASP A:315 , ARG A:600 , ARG A:662 , TYR A:695binding site for residue PO4 A 802
3AC3SOFTWARELEU A:276 , TYR A:278 , TYR A:288 , PHE A:289 , THR A:313 , MET A:723 , ASN A:725 , VAL A:726 , VAL A:727 , HOH A:906 , HOH A:956binding site for residue PEG A 803
4AC4SOFTWAREARG B:290 , ILE B:291 , ARG B:309 , ASP B:315 , ASP B:372 , ASP B:388 , PHE B:396 , TYR B:553 , SER B:582 , ARG B:600 , ARG B:662 , TYR B:695 , HOH B:967 , HOH B:1054 , HOH B:1061binding site for residue DAN B 801
5AC5SOFTWARELEU B:128 , PHE B:149 , ARG B:151 , GLU B:159 , ARG B:161 , ARG B:237 , PHE B:243 , HOH B:950 , HOH B:1215binding site for residue SIA B 802
6AC6SOFTWARELYS B:209 , VAL B:211 , GLU B:212 , GLU B:352 , LYS B:724 , HOH B:908 , HOH B:948 , HOH B:1040binding site for residue GOL B 803
7AC7SOFTWARETYR B:288 , PHE B:289 , MET B:723 , ASN B:725 , VAL B:726 , HOH B:992binding site for residue PEG B 804

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YW1)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Phe A:316 -Leu A:317
2Glu A:471 -Asn A:472
3Phe B:316 -Leu B:317

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YW1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YW1)

(-) Exons   (0, 0)

(no "Exon" information available for 4YW1)

(-) 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:659
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee...eehhhhhh.......eeeeeeeee......eeeeeee.........eeeeee.....eeeeeee....eeeeeee......ee..ee..eeeeeeee....eeeeee..eeeeeee.....hhhhh....eeee..eee..eee...eeeeeeeeee....hhhhhhhhhh..hhhhh...........eeeeeeeee.....eeeeeeee..........eeeeeeee..........eeee................hhhhh......eeeeeeeee.....eeeeeeee...............eeee..eeeeeeee.......eee....eeee....eeeeeee.....eee..ee.eeeeeeee......eeeeeeeeee.........ee.....eeeeeee..........ee............ee..ee.ee......eeeeee...eeeeeee.......eeeeee........eeeeeee..eeeeee.......eeeee..........ee.............eeeeeeeee..eeeeeeeee........eeeeeeee.....eeeeeeeee.........eeeee.....eeeee..................eeeehhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yw1 A  83 ETPVLEKNNVTLTGGGENVTKELKDKFTSGDFTVVIKYNQSSEKGLQALFGISNSKPGQQNSYVDVFLRDNGELGMEARDTSSNKNNLVSRPASVWGKYKQEAVTNTVAVVADSVKKTYSLYANGTKVVEKKVDNFLNIKDIKGIDYYMLGGVKRAGKTAFGFNGTLENIKFFNSALDEETVKKMTTNAVTGHLIYTANDTTGSNYFRIPVLYTFSNGRVFSSIDARYGGTHDFLNKINIATSYSDDNGKTWTKPKLTLAFDDFAPVPLEWPREVGGRDLQISGGATYIDSVIVEKKNKQVLMFADVMPAGVSFREATRKDSGYKQIDGNYYLKLRKQGDTDYNYTIRENGTVYDDRTNRPTEFSVDKNFGIKQNGNYLTVEQYSVSFENNKKTEYRNGTKVHMNIFYKDALFKVVPTNYIAYISSNDHGESWSAPTLLPPIMGLNRNAPYLGPGRGIIESSTGRILIPSYTGKESAFIYSDDNGASWKVKVVPLPSSWSAEAQFVELSPGVIQAYMRTNNGKIAYLTSKDAGTTWSAPEYLKFVSNPSYGTQLSIINYSQLIDGKKAVILSTPNSTNGRKHGQIWIGLINDDNTIDWRYHHDVDYSNYGYSYSTLTELPNHEIGLMFEKFDSWSRNELHMKNVVPYITFKIEDLKKNL 741
                                    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       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732         


Chain B from PDB  Type:PROTEIN  Length:659
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee...ee.............eeeeeeeee......eeeeeee.........eeeeee.....eeeeeee....eeeeeee......ee..ee..eeeeeeee....eeeeee..eeeeeee.....hhhhh....eeee..eee..eee...eeeeeeeeee....hhhhhhhhhh..hhhhh...........eeeeeeeee.....eeeeeeee..........eeeeeeee..........eeee................hhhhh......eeeeeeeee.....eeeeeeee...............eeee..eeeeeeee.......eee....eeee....eeeeeee.....eee..ee.eeeeeeee......eeeeeeeeee.........ee.....eeeeeee..........ee............ee..ee.ee......eeeeee...eeeeeee.......eeeeee........eeeeeee..eeeeee.......eeeee..........ee.............eeeeeeeee..eeeeeeeee........eeeeeeee.....eeeeeeeee.........eeeee.....eeeee..................eeeehhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yw1 B  83 ETPVLEKNNVTLTGGGENVTKELKDKFTSGDFTVVIKYNQSSEKGLQALFGISNSKPGQQNSYVDVFLRDNGELGMEARDTSSNKNNLVSRPASVWGKYKQEAVTNTVAVVADSVKKTYSLYANGTKVVEKKVDNFLNIKDIKGIDYYMLGGVKRAGKTAFGFNGTLENIKFFNSALDEETVKKMTTNAVTGHLIYTANDTTGSNYFRIPVLYTFSNGRVFSSIDARYGGTHDFLNKINIATSYSDDNGKTWTKPKLTLAFDDFAPVPLEWPREVGGRDLQISGGATYIDSVIVEKKNKQVLMFADVMPAGVSFREATRKDSGYKQIDGNYYLKLRKQGDTDYNYTIRENGTVYDDRTNRPTEFSVDKNFGIKQNGNYLTVEQYSVSFENNKKTEYRNGTKVHMNIFYKDALFKVVPTNYIAYISSNDHGESWSAPTLLPPIMGLNRNAPYLGPGRGIIESSTGRILIPSYTGKESAFIYSDDNGASWKVKVVPLPSSWSAEAQFVELSPGVIQAYMRTNNGKIAYLTSKDAGTTWSAPEYLKFVSNPSYGTQLSIINYSQLIDGKKAVILSTPNSTNGRKHGQIWIGLINDDNTIDWRYHHDVDYSNYGYSYSTLTELPNHEIGLMFEKFDSWSRNELHMKNVVPYITFKIEDLKKNL 741
                                    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       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732
   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  (0, 0)

(no "SCOP Domain" information available for 4YW1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YW1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YW1)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4YW1)

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 Related Entries

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UniProtKB/TrEMBL
        A0A0H2UQE4_S | A0A0H2UQE4: 4yw2 4yw3 4yw5 4yz1 4yz2 4yz3 4yz4 4yz5

(-) Related Entries Specified in the PDB File

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