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(-) Description

Title :  ANTIBODY FAB COMPLEXED WITH PHENCYCLIDINE
 
Authors :  K. Lim, S. M. Owens, L. Arnold, J. C. Sacchettini, D. S. Linthicum
Date :  02 Jun 98  (Deposition) - 27 Jan 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Immunoglobulin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Lim, S. M. Owens, L. Arnold, J. C. Sacchettini, D. S. Linthicum
Crystal Structure Of Monoclonal 6B5 Fab Complexed With Phencyclidine.
J. Biol. Chem. V. 273 28576 1998
PubMed-ID: 9786848  |  Reference-DOI: 10.1074/JBC.273.44.28576
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN
    Chains: A, C
    Fragment: FAB
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: COMPLEXED WITH 1-(1-PHENYLCYCLOHEXYL) PIPERIDINE (PCP, OR PHENCYCLIDINE)
 
Molecule 2 - IMMUNOGLOBULIN
    Chains: B, D
    Fragment: FAB
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: COMPLEXED WITH 1-(1-PHENYLCYCLOHEXYL) PIPERIDINE (PCP, OR PHENCYCLIDINE)

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
11PC2Ligand/Ion1-(PHENYL-1-CYCLOHEXYL)PIPERIDINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
11PC1Ligand/Ion1-(PHENYL-1-CYCLOHEXYL)PIPERIDINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
11PC1Ligand/Ion1-(PHENYL-1-CYCLOHEXYL)PIPERIDINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:32 , GLY A:91 , TYR A:96 , HIS B:35 , SER B:95 , TRP B:97 , ASP B:98 , PHE B:100BINDING SITE FOR RESIDUE 1PC B 227
2AC2SOFTWAREGLY C:91 , TYR C:96 , TYR D:33 , HIS D:35 , TYR D:50 , SER D:95 , TRP D:97 , ASP D:98 , PHE D:100BINDING SITE FOR RESIDUE 1PC C 212

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:92
4B:142 -B:208
5C:23 -C:88
6C:134 -C:194
7D:22 -D:92
8D:142 -D:208

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Thr A:7 -Pro A:8
2Ala A:94 -Pro A:95
3Tyr A:140 -Pro A:141
4Phe B:148 -Pro B:149
5Arg B:199 -Pro B:200
6Thr C:7 -Pro C:8
7Ala C:94 -Pro C:95
8Tyr C:140 -Pro C:141
9Phe D:148 -Pro D:149
10Arg D:199 -Pro D:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PCP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PCP)

(-) Exons   (0, 0)

(no "Exon" information available for 2PCP)

(-) 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:216
                                                                                                                                                                                                                                                        
               SCOP domains d2pcpa1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d2pcpa2 A:108-211 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 2pcpA01 A:1-108 Immunoglobulins                                                                                  2pcpA02 A:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..........eeeeeeee............eeeeee.....eeeeee............eeeeee..eeeeeee...hhh.eeeeeee...........eee.........eeeee...hhhhhh.eeeeeeeee........eeeee..eee...eeeee...........eeeeeeeehhhhh...eeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pcp A   1 DVLMTQTPLSLPVSLGDQASISCRSSQTIVHSNGNTYLEWYLQKPGQSPKLLIYKVTNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGTHAPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 211
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205      
                                                     27A||||                                                                                                                                                                                        
                                                      27B|||                                                                                                                                                                                        
                                                       27C||                                                                                                                                                                                        
                                                        27D|                                                                                                                                                                                        
                                                         27E                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d2pcpb1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                       d2pcpb2 B:114-226 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                    SCOP domains
               CATH domains 2pcpB01 B:1-113 Immunoglobulins                                                                                      2pcpB02 B:114-226 Immunoglobulins                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee....eeeeeeeee.......eeeeeeee...eeeeeeeee....eeee.......eeeeee....eeeeeee...hhh.eeeeeeee...........eeeee........eeeee..........eeeeeeeee.......eeeehhh.....eee...eee..eeeeeeeeeee..........eeeeehhh.eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pcp B   1 EVQLQQSGPELVKPGASVKMSCKASGYTFTDYYIHWNKQSHGKSLEWIGYIYPNNGGNGYNHKFKGKATLTVDKSSSTAYMDVRTLTSEDSAVYYCGRSTWDDFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSPRPSETVTCNVAHPASSTKVDKKIV 226
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126      |138       148     ||163     ||174     ||186       196| ||   209       219   ||
                                                                              52A                            82A||                                                133|               154|||    169|      180|          196| || 206|            223|
                                                                                                              82B|                                                 136                156||     171       183           198 ||  208             226
                                                                                                               82C                                                                     157|                               200|                     
                                                                                                                                                                                        162                                202                     


Chain C from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d2pcpc1 C:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d2pcpc2 C:108-211 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 2pcpC01 C:1-108 Immunoglobulins                                                                                  2pcpC02 C:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee......eeeee............eeeeee..eeeeee....hhh.eeeeeee...........eeeeee......eeee....hhhhh..eeeeeeeee.......eeeeee........eeeee...........eeeeeeeehhhhhh..eeeeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pcp C   1 DVLMTQTPLSLPVSLGDQASISCRSSQTIVHSNGNTYLEWYLQKPGQSPKLLIYKVTNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGTHAPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 211
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205      
                                                     27A||||                                                                                                                                                                                        
                                                      27B|||                                                                                                                                                                                        
                                                       27C||                                                                                                                                                                                        
                                                        27D|                                                                                                                                                                                        
                                                         27E                                                                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d2pcpd1 D:1-113 Immunoglobulin heavy chain variable domain, VH                                                       d2pcpd2 D:114-226 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                    SCOP domains
               CATH domains 2pcpD01 D:1-113 Immunoglobulins                                                                                      2pcpD02 D:114-226 Immunoglobulins                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....eee.....eeeeeeee.......eeeeeee.....eeeeeeee....eeee.......eeeeee....eeeeee....hhh..eeeeeee....eeee.....eee.........eeee..........eeeeeeeeeee.........hhh.................eeeeeeeeee.........eeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pcp D   1 EVQLQQSGPELVKPGASVKMSCKASGYTFTDYYIHWNKQSHGKSLEWIGYIYPNNGGNGYNHKFKGKATLTVDKSSSTAYMDVRTLTSEDSAVYYCGRSTWDDFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSPRPSETVTCNVAHPASSTKVDKKIV 226
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126      |138       148     ||163     ||174     ||186       196| ||   209       219   ||
                                                                              52A                            82A||                                                133|               154|||    169|      180|          196| || 206|            223|
                                                                                                              82B|                                                 136                156||     171       183           198 ||  208             226
                                                                                                               82C                                                                     157|                               200|                     
                                                                                                                                                                                        162                                202
   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  (4, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
House mouse (Mus musculus) (616)
1a2pcpA02A:109-211
1b2pcpA01A:1-108
1c2pcpC01C:1-108
1d2pcpB02B:114-226
1e2pcpD02D:114-226
1f2pcpB01B:1-113
1g2pcpD01D:1-113
1h2pcpC02C:109-211

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2PCP)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2PCP)

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