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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PROTEASE DOMAIN OF BOTULINUM NEUROTOXIN SEROTYPE A WITH A PEPTIDE INHIBITOR RRGF
 
Authors :  D. Kumaran, S. Swaminathan
Date :  26 Feb 11  (Deposition) - 08 Feb 12  (Release) - 23 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Endopeptidase, Syntaxin, Bio-Warfare Agent, Membrane, Metal-Binding, Metalloprotease, Protease, Secreted, Transmembrane, Snap25, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Kumar, D. Kumaran, S. A. Ahmed, S. Swaminathan
Peptide Inhibitors Of Botulinum Neurotoxin Serotype A: Design, Inhibition, Cocrystal Structures, Structure-Activit Relationship And Pharmacophore Modeling.
Acta Crystallogr. , Sect. D V. 68 511 2012
PubMed-ID: 22525749  |  Reference-DOI: 10.1107/S0907444912003551

(-) Compounds

Molecule 1 - BOTULINUM NEUROTOXIN TYPE A
    ChainsA
    EC Number3.4.24.69
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21(DE3)RIL
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentLIGHT CHAIN (UNP RESIDUES 1-424)
    GeneBOTA, CBO0806, CLC_0862
    Organism ScientificCLOSTRIDIUM BOTULINUM
    Organism Taxid441771
    StrainHALL / ATCC 3502 / NCTC 13319 / TYPE A
    SynonymBONT/A, BONTOXILYSIN-A, BOTOX
 
Molecule 2 - INHIBITORY PEPTIDE RRGF
    ChainsB
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1NH21Mod. Amino AcidAMINO GROUP
2SO43Ligand/IonSULFATE ION
3ZN1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:223 , HIS A:227 , GLU A:262 , ARG B:196BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWARELYS A:340BINDING SITE FOR RESIDUE SO4 A 502
3AC3SOFTWAREASN A:174 , LEU A:175 , THR A:176 , ARG A:177 , ASN A:394 , HOH A:627BINDING SITE FOR RESIDUE SO4 A 503
4AC4SOFTWAREARG A:231 , PRO A:239 , HOH A:641 , HOH A:709 , ARG B:196BINDING SITE FOR RESIDUE SO4 A 504
5AC5SOFTWAREPHE A:163 , GLU A:164 , PHE A:194 , THR A:215 , HIS A:223 , GLU A:224 , HIS A:227 , TYR A:251 , GLU A:262 , ARG A:363 , TYR A:366 , ASN A:368 , PHE A:369 , ASP A:370 , ZN A:501 , SO4 A:504 , HOH A:640 , HOH A:699 , HOH B:701 , HOH B:702 , HOH B:703 , HOH B:704 , HOH B:705BINDING SITE FOR CHAIN B OF INHIBITORY PEPTIDE RRGF

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QW5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QW5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QW5)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.BXA1_CLOBH220-229  1A:220-229

(-) Exons   (0, 0)

(no "Exon" information available for 3QW5)

(-) 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:423
 aligned with BXA1_CLOBH | A5HZZ9 from UniProtKB/Swiss-Prot  Length:1296

    Alignment length:423
                                    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       420   
           BXA1_CLOBH     1 MPFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNFTGLF 423
               SCOP domains d3qw5a_ A: Botulinum neurotoxin                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeee.........eeeeeee..eeeeeee..............hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........ee..hhh.eeeee.....eeeee..eeeee........eee.................eeee....eeeee..hhhhhh........ee.hhhhhhhhhhhhhhhhhh........eee...hhhhhhh..eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhh..ee.....ee.hhhhhhhhhhhhhh..hhhhhhhhhh............eeee.........................hhhhh...hhhhheeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qw5 A   1 MPFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNFTGLF 423
                                    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       420   

Chain B from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 3qw5 B 196 RRGFx 200
                                |
                              200-NH2

   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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QW5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QW5)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BXA1_CLOBH | A5HZZ9)
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:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds 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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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.
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0044164    host cell cytosol    The part of the host cell cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0044156    host cell junction    A plasma membrane part that forms a specialized region of connection between two host cells or between a host cell and the host extracellular matrix. At a host cell junction, anchoring proteins extend through the host plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    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:0044231    host cell presynaptic membrane    A specialized area of membrane of the host axon terminal that faces the plasma membrane of the host neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many host synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.
    GO:0044221    host cell synapse    The junction between a nerve fiber of one host neuron and another host neuron or muscle fiber or glial cell; the site of interneuronal communication.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BXA1_CLOBH | A5HZZ91xtf 1xtg 2w2d 3bwi 3c8a 3c8b 3dda 3ddb 3ds9 3dse 3k3q 3qix 3qiy 3qiz 3qj0 3qw6 3qw7 3qw8 4ks6 4ktx 4kuf

(-) Related Entries Specified in the PDB File

3bwi 3c88 3c89 3c8a 3c8b 3dda 3ddb 3qw6 3qw7 3qw8