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(-) Description

Title :  STRUCTURE OF A SINGLE-DOMAIN CAMELID ANTIBODY FRAGMENT CAB-F11N 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 :  04 Oct 13  (Deposition) - 08 Oct 14  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Immunoglobulin Fold, Antigen Binding, 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
    Chains: A, C
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNY
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 44-307
    Gene: PENP, BLAP
    Mutation: YES
    Organism Scientific: BACILLUS LICHENIFORMIS
    Organism Taxid: 1402
    Synonym: PENICILLINASE, LARGE EXOPENICILLINASE, SMALL EXOPENICILLINASE
 
Molecule 2 - CAMELID HEAVY-CHAIN ANTIBODY VARIABLE FRAGMENT CAB-F11N
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMES4
    Expression System Strain: TG1
    Expression System Taxid: 562
    Expression System Vector Type: PHAGEMID
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4N1H)

(-) Sites  (0, 0)

(no "Site" information available for 4N1H)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1B:22 -B:96
2D:22 -D:96

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:166 -Pro A:167
2Glu C:166 -Pro C:167
3Asp C:197 -Pro C:197A

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N1H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N1H)

(-) Exons   (0, 0)

(no "Exon" information available for 4N1H)

(-) 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:257
                                                                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhheeeeeeeee.....eeee....eee...hhhhhhhhhhhhhhhhhhhh.ee............hhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhh........eeehhhhhhhhhhhhh.....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeeee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4n1h A   31 DDFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALVTSLRAFALEPGKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN  291
                                    40        50      ||61        71        81 ||     93       103       113       123       133       143       153       163       173       183       193   ||  202       212       222       232     ||243       254       264       274       284       
                                                     57|                      83|                                                                                                           197A|                                      238|         252|                                     
                                                      59                       86                                                                                                            197B                                       240          254                                     


Chain B from PDB  Type:PROTEIN  Length:126
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eee.....eeeeeee...hhhhheeeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee..........hhhhh.......eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                4n1h B    1 QVQLQESGGGLVQAGASLKLSCAASGRTFSSYAMGWFRQAPGKEREFVAAISRSGGDTKYADSVKGRFAISRDNDKNTVWLRMNSLKPEDTAVYYCAATTYASLSDTYIGEHIYDDWGQGTQVTVS  126
                                    10        20        30        40        50        60        70        80        90       100       110       120      


Chain C from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhh..eeeeeeee.....eeee.....ee...hhhhhhhhhhhhhh.hhhhh.ee..hhhhh.....hhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh......hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4n1h C   31 DDFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALVTSLRAFALEDPGKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN  291
                                    40        50      ||61        71        81 ||     93       103       113       123       133       143       153       163       173       183       193    || 201       211       221       231      |242       252|      263       273       283        
                                                     57|                      83|                                                                                                            197A|                                      238|         252|                                     
                                                      59                       86                                                                                                             197B                                       240          254                                     


Chain D from PDB  Type:PROTEIN  Length:126
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..........eeeeeeee.......eeeeeee......eeeeee......eee.......ee..ee....eeeeee...hhhhheeeeeeee..........hhhhh.ee...eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                4n1h D    1 QVQLQESGGGLVQAGASLKLSCAASGRTFSSYAMGWFRQAPGKEREFVAAISRSGGDTKYADSVKGRFAISRDNDKNTVWLRMNSLKPEDTAVYYCAATTYASLSDTYIGEHIYDDWGQGTQVTVS  126
                                    10        20        30        40        50        60        70        80        90       100       110       120
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4N1H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N1H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N1H)

(-) Gene Ontology  (6, 6)

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  Cis Peptide Bonds
    Asp C:197 - Pro C:197A  [ RasMol ]  
    Glu A:166 - Pro A:167   [ RasMol ]  
    Glu C:166 - Pro C:167   [ RasMol ]  
 
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  3.5.2.6
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 Related Entries

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

UniProtKB/Swiss-Prot
        BLAC_BACLI | P00808: 1i2s 1i2w 1mbl 1w7f 2blm 2wk0 2y91 3b3x 3ly3 3ly4 3m2j 3m2k 3sh7 3sh8 3sh9 3soi 4blm 4m3k 4n92 4n9k 4n9l 5ghx 5ghy 5ghz

(-) Related Entries Specified in the PDB File

4m3j 4m3k