Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  ALPHA-BUNGAROTOXIN COMPLEXED WITH HIGH AFFINITY PEPTIDE
 
Authors :  M. Harel, R. Kasher, J. L. Sussman
Date :  02 May 01  (Deposition) - 10 Nov 01  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Toxin/Peptide, Complex (Toxin-Peptide), Acetylcholine Receptor Mimitope, Alpha-Bungarotoxin, 3- Finger, Protein-Peptide Complex, Toxin, Toxin-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Harel, R. Kasher, A. Nicolas, J. M. Guss, M. Balass, M. Fridkin, A. B. Smit, K. Brejc, T. K. Sixma, E. Katchalski-Katzir, J. L. Sussman, S. Fuchs
The Binding Site Of Acetylcholine Receptor As Visualized In The X-Ray Structure Of A Complex Between Alpha-Bungarotoxin And A Mimotope Peptide.
Neuron V. 32 265 2001
PubMed-ID: 11683996  |  Reference-DOI: 10.1016/S0896-6273(01)00461-5

(-) Compounds

Molecule 1 - ALPHA-BUNGAROTOXIN ISOFORM V31
    ChainsA
    Organism CommonMANY-BANDED KRAIT
    Organism ScientificBUNGARUS MULTICINCTUS
    Organism Taxid8616
    Other DetailsALPHA-NEUROTOXIN
    SecretionVENOM
    SynonymALPHA-BTX V31, ALPHA-BGT(V31), BGTX V31, LONG NEUROTOXIN 1
 
Molecule 2 - ALPHA-BUNGAROTOXIN ISOFORM A31
    ChainsB
    Organism CommonMANY-BANDED KRAIT
    Organism ScientificBUNGARUS MULTICINCTUS
    Organism Taxid8616
    SecretionVENOM
    SynonymALPHA-BTX A31, ALPHA-BGT(A31), BGTX A31, LONG NEUROTOXIN 1
 
Molecule 3 - PEPTIDE INHIBITOR
    ChainsC, D
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    Other DetailsA SYNTHESIZED PEPTIDE MIMICKING ACHR LOOP THAT INHIBITS A-BTX BINDING TO ACHR
    Other Details - SourceMIMOTOPE OF THE NICOTINIC ACETYLCHOLINE RECEPTOR
    SynonymHIGH AFFINITY PEPTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1IOD2Ligand/IonIODIDE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1IOD1Ligand/IonIODIDE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1IOD1Ligand/IonIODIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:25 , THR A:58 , HOH A:2081BINDING SITE FOR RESIDUE IOD A 1075
2AC2SOFTWAREARG B:25 , MET B:27 , GLU B:56 , THR B:58BINDING SITE FOR RESIDUE IOD B 1075

(-) SS Bonds  (11, 11)

Asymmetric Unit
No.Residues
1A:3 -A:23
2A:16 -A:44
3A:29 -A:33
4A:48 -A:59
5A:59 -A:59
6A:60 -A:65
7B:3 -B:23
8B:16 -B:44
9B:29 -B:33
10B:48 -B:59
11B:60 -B:65

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:9 -Pro A:10
2Ser B:9 -Pro B:10

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HC9)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SNAKE_TOXINPS00272 Snake toxins signature.3L21A_BUNMU64-84  1B:43-63
3L21V_BUNMU64-84  1A:43-63
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SNAKE_TOXINPS00272 Snake toxins signature.3L21A_BUNMU64-84  0-
3L21V_BUNMU64-84  1A:43-63
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SNAKE_TOXINPS00272 Snake toxins signature.3L21A_BUNMU64-84  1B:43-63
3L21V_BUNMU64-84  0-

(-) Exons   (0, 0)

(no "Exon" information available for 1HC9)

(-) 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:74
 aligned with 3L21V_BUNMU | P60616 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:74
                                    31        41        51        61        71        81        91    
           3L21V_BUNMU   22 IVCHTTATSPISAVTCPPGENLCYRKMWCDVFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNPHPKQRPG 95
               SCOP domains d1hc9a_ A: Bungarotoxin                                                    SCOP domains
               CATH domains 1hc9A00 A:1-74 CD59                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eeee......eeeeeee...hhhhhh.eeeeeee..........eeeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------SNAKE_TOXIN          ----------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------- Transcript
                  1hc9 A  1 IVCHTTATSPISAVTCPPGENLCYRKMWCDVFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNPHPKQRPG 74
                                    10        20        30        40        50        60        70    

Chain B from PDB  Type:PROTEIN  Length:74
 aligned with 3L21A_BUNMU | P60615 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:74
                                    31        41        51        61        71        81        91    
           3L21A_BUNMU   22 IVCHTTATSPISAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNPHPKQRPG 95
               SCOP domains d1hc9b_ B: Bungarotoxin                                                    SCOP domains
               CATH domains 1hc9B00 B:1-74 CD59                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eeee......eeeeeee...hhhhhh.eeeeeee..........eeeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------SNAKE_TOXIN          ----------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                  1hc9 B  1 IVCHTTATSPISAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNPHPKQRPG 74
                                    10        20        30        40        50        60        70    

Chain C from PDB  Type:PROTEIN  Length:13
                                            
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author .eee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                  1hc9 C  1 WRYYESSLLPYPD 13
                                    10   

Chain D from PDB  Type:PROTEIN  Length:12
                                           
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ..ee........ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                  1hc9 D  1 WRYYESSLLPYP 12
                                    10  

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HC9)

(-) Gene Ontology  (4, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (3L21V_BUNMU | P60616)
biological process
    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.
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:0035792    other organism postsynaptic membrane    A postsynaptic membrane that is part of another organism, i.e. a secondary organism with which the first organism is interacting. A postsynaptic membrane is a specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters transmit the signal across the synaptic cleft to the postsynaptic membrane.

Chain B   (3L21A_BUNMU | P60615)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    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.
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:0035792    other organism postsynaptic membrane    A postsynaptic membrane that is part of another organism, i.e. a secondary organism with which the first organism is interacting. A postsynaptic membrane is a specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters transmit the signal across the synaptic cleft to the postsynaptic membrane.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    IOD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:9 - Pro A:10   [ RasMol ]  
    Ser B:9 - Pro B:10   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1hc9
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  3L21A_BUNMU | P60615
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  3L21V_BUNMU | P60616
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  3L21A_BUNMU | P60615
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  3L21V_BUNMU | P60616
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        3L21A_BUNMU | P606151abt 1bxp 1haa 1haj 1hoy 1idg 1idh 1idi 1idl 1ik8 1ikc 1jbd 1kc4 1kfh 1kl8 1l4w 1ljz 1lk1 1rgj 2abx 2btx
        3L21V_BUNMU | P606161haa 1haj 1lk1 2qc1 4hqp 4uy2 5hbt 5hbv

(-) Related Entries Specified in the PDB File

1abt ALPHA-BUNGAROTOXIN COMPLEXED WITH THE 185 - 196 FRAGMENT OF THE ALPHA-SUBUNIT OF THE TORPEDO NICOTINIC ACETYLCHOLINE RECEPTOR (NMR, 4 STRUCTURES)
1bxp SOLUTION NMR STRUCTURE OF THE COMPLEX OF ALPHA-BUNGAROTOXIN WITH A LIBRARY DERIVED PEPTIDE, 20 STRUCTURES
1haa A BETA-HAIRPIN STRUCTURE IN A 13-MER PEPTIDE THAT BINDS A- BUNGAROTOXIN WITH HIGH AFFINITY AND NEUTRALIZES ITS TOXICITY
1haj A BETA-HAIRPIN STRUCTURE IN A 13-MER PEPTIDE THAT BINDS A- BUNGAROTOXIN WITH HIGH AFFINITY AND NEUTRALIZES ITS TOXICITY
1hn7 NMR STRUCTURE OF THE COMPLEX BETWEEN A-BUNGAROTOXIN AND AMIMOTOPE OF THE NICOTINIC ACETILCHOLINE RECEPTOR
1hoy NMR STRUCTURE OF THE COMPLEX BETWEEN A-BUNGAROTOXIN AND AMIMOTOPE OF THE NICOTINIC ACETILCHOLINE RECEPTOR
1idg THE NMR SOLUTION STRUCTURE OF THE COMPLEX FORMED BETWEEN ALPHA- BUNGAROTOXIN AND AN 18MER COGNATE PEPTIDE
1idh THE NMR SOLUTION STRUCTURE OF THE COMPLEX FORMED BETWEEN ALPHA- BUNGAROTOXIN AND AN 18MER COGNATE PEPTIDE
1idi THE NMR SOLUTION STRUCTURE OF ALPHA-BUNGAROTOXIN
1idl THE NMR SOLUTION STRUCTURE OF ALPHA-BUNGAROTOXIN
2btx SOLUTION NMR STRUCTURE OF THE COMPLEX OF ALPHA-BUNGAROTOXIN WITH A LIBRARY DERIVED PEPTIDE, NMR, MINIMIZED AVERAGE STRUCTURE