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

(-) Description

Title :  STRUCTURE OF A SINGLE DOMAIN CAMELID ANTIBODY FRAGMENT CAB-H7S IN COMPLEX WITH THE BLAP BETA-LACTAMASE FROM BACILLUS LICHENIFORMIS
 
Authors :  C. Pain, F. Kerff, R. Herman, E. Sauvage, S. Preumont, P. Charlier, M. Du
Date :  06 Aug 13  (Deposition) - 06 Aug 14  (Release) - 06 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.48
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Immunoglobulin Fold, Antigen Binding, Beta-Lactamase-Antibody Complex, Hydrolase-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Pain, A. Cosolo, S. Preumont, N. Scarafone, D. Thorn, R. Herman, H. Spiegel, E. Pardon, A. Matagne, P. Charlier, J. Steyaert, C. Damblon, F. Kerff, G. Esposito, M. Dumoulin
Probing The Mechanism Of Aggregation Of Polyq Model Protein With Camelid Heavy-Chain Antibody Fragments
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    ChainsA
    EC Number3.5.2.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNY
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 44-307
    GenePENP, BLAP
    Organism ScientificBACILLUS LICHENIFORMIS
    Organism Taxid1402
    SynonymPENICILLINASE, LARGE EXOPENICILLINASE, SMALL EXOPENICILLINASE
 
Molecule 2 - CAMELID HEAVY-CHAIN ANTIBODY VARIABLE FRAGMENT CAB-H7S
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMES4
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificLAMA GLAMA
    Organism Taxid9844

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:136 , LYS A:140 , HOH A:502 , TYR B:37 , ARG B:45BINDING SITE FOR RESIDUE CL A 401
2AC2SOFTWARELYS A:269 , THR B:32 , ASN B:52 , SER B:53BINDING SITE FOR RESIDUE CL B 201

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:22 -B:95

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:166 -Pro A:167
2Asp A:197 -Pro A:197A

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M3K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M3K)

(-) Exons   (0, 0)

(no "Exon" information available for 4M3K)

(-) 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:260
                                                                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..eeeeeeee.....eeee.....ee...hhhhhhhhhhhhhh.hhhhh.eee.hhhhh.....hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh......hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m3k A   29 MKDDFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALVTSLRAFALEDPGKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN  291
                                    38        48        59        69        79   ||   91       101       111       121       131       141       151       161       171       181       191      |199       209       219       229       240       250 ||    261       271       281       291
                                                       57|                      83|                                                                                                            197A|                                      238|         252|                                     
                                                        59                       86                                                                                                             197B                                       240          254                                     

Chain B from PDB  Type:PROTEIN  Length:116
                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eee.....eeeeeeee..eeeeeeeeeeee...eeeeee.....eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeeeee....eeeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                4m3k B    2 VQLQESGGGLVQPGGSLRLSCAASGSISSITTMGWYRQDGRELVALINSVGDTTYAGSVKGRFTISRDNAKNTVYLEMSSLKPEDTAVYYCNAFMSTNSGRTGSFWGQGTQVTVSS  120
                                    11        21        31        44        54        64        74        84        94       104       114      
                                                                 40|                                                                            
                                                                  44                                                                            

   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 4M3K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M3K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M3K)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:197 - Pro A:197A  [ RasMol ]  
    Glu A:166 - Pro A:167   [ RasMol ]  
 

(-) 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
  4m3k
    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
  BLAC_BACLI | P00808
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.5.2.6
    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
  BLAC_BACLI | P00808
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        BLAC_BACLI | P008081i2s 1i2w 1mbl 1w7f 2blm 2wk0 2y91 3b3x 3ly3 3ly4 3m2j 3m2k 3sh7 3sh8 3sh9 3soi 4blm 4n1h 4n92 4n9k 4n9l 5ghx 5ghy 5ghz

(-) Related Entries Specified in the PDB File

4m3j