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(-) Description

Title :  CRYSTAL STRUCTURE OF BONT/A LC WITH JTH-NB-7239 PEPTIDE
 
Authors :  J. E. Zuniga
Date :  09 Jun 10  (Deposition) - 21 Jul 10  (Release) - 21 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A,C  (1x)
Keywords :  Botulinum Neurotoxin, Snare, Botulism, Inhibition, Metalloprotease, Neurotransmission, Neuromuscular Junction, Hydrolase, Membrane, Metal-Binding, Protease, Secreted, Toxin, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. Zuniga, J. T. Hammill, O. Drory, J. E. Nuss, J. C. Burnett, R. Gussio, P. Wipf, S. Bavari, A. T. Brunger
Iterative Structure-Based Peptide-Like Inhibitor Design Against The Botulinum Neurotoxin Serotype A.
Plos One V. 5 E1137 2010
PubMed-ID: 20614028  |  Reference-DOI: 10.1371/JOURNAL.PONE.0011378

(-) Compounds

Molecule 1 - BONT/A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: LIGHT CHAIN, RESIDUES 1-420
    Gene: BONT/A, BONT/A, BONTA
    Organism Scientific: CLOSTRIDIUM BOTULINUM
    Organism Taxid: 1491
    Synonym: BONT/A1, BOTULINUM NEUROTOXIN TYPE A, NEUROTOXIN A, NEUROTOXIN BONT
 
Molecule 2 - JTH-NB72-39 INHIBITOR
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AC
Biological Unit 1 (1x): AC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1AIB1Mod. Amino AcidALPHA-AMINOISOBUTYRIC ACID
2NI1Ligand/IonNICKEL (II) ION
3ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1AIB1Mod. Amino AcidALPHA-AMINOISOBUTYRIC ACID
2NI-1Ligand/IonNICKEL (II) ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:223 , HIS A:227 , GLU A:262 , ARG C:1BINDING SITE FOR RESIDUE ZN A 600
2AC2SOFTWAREGLU A:64 , HIS A:269 , LYS A:272 , HOH A:459 , HOH A:502 , HOH A:503 , HOH A:504 , HOH A:505BINDING SITE FOR RESIDUE NI A 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NF3)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Val A:68 -Pro A:69
2Glu A:197 -Glu A:198
3Ala A:308 -Ser A:309

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NF3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NF3)

(-) Exons   (0, 0)

(no "Exon" information available for 3NF3)

(-) 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:392
 aligned with Q7B8V4_CLOBO | Q7B8V4 from UniProtKB/TrEMBL  Length:1296

    Alignment length:417
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       
         Q7B8V4_CLOBO     1 MPFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLK 417
               SCOP domains d3nf3a_ A: Botulinum neuro  toxin                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -Peptidase_M27-3nf3A01 A:2  -410                                                                                                                                                                                                                                                                                                                                                                                          ------- Pfam domains
         Sec.struct. author ..................eeeee...--....eeeeeee..eeeeeee...........-...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........ee..hhh.eeeee.....eeeee..eeeee........eee.................eeee....eeeee..------------..ee.hhhhhhhhhhhhhhhhhh........eee..---------.eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee...-.hhhhhhhhhhhhh.eee.....eeehhhhhhhhhhhhhhh.hhhhhhhhhh..........eeeeee.........................hhhhh........ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nf3 A   1 MPFVNKQFNYKDPVNGVDIAYIKIPN--QMQPVKAFKIHNKIWVIPERDTFTNPEEGDL-PPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEE------------GKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVN---------LEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGT-ASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLK 417
                                    10        20     |  30        40        50        |-|       70        80        90       100       110       120       130       140       150       160       170       180       190       | -         -|      220       230       240     |   -     | 260       270       280       290       300     | 310       320       330       340       350       360       370       380       390       400       410       
                                                    26 29                            59 |                                                                                                                                      198          211                                246       256                                               306 |                                                                                                             
                                                                                       61                                                                                                                                                                                                                                                    308                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author .hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 3nf3 C   1 RRFaAMLA   8
                               |    
                               4-AIB
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NF3)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Peptidase_MA (251)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q7B8V4_CLOBO | Q7B8V4)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0051609    inhibition of neurotransmitter uptake    Any process that prevents the activation of the directed movement of a neurotransmitter into a cell.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q7B8V4_CLOBO | Q7B8V4: 2ilp 2ima 2imb 2imc 3v0a 3v0b 3v0c
UniProtKB/TrEMBL
        Q7B8V4_CLOBO | Q7B8V4: 2ise 2isg 2ish

(-) Related Entries Specified in the PDB File

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