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(-) Description

Title :  CRYSTAL STRUCTURES OF AN ANTIBODY TO A PEPTIDE AND ITS COMPLEX WITH PEPTIDE ANTIGEN AT 2.8 ANGSTROMS
 
Authors :  R. L. Stanfield, I. A. Wilson
Date :  21 Mar 91  (Deposition) - 15 Apr 92  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  H,J,L,M
Keywords :  Immunoglobulin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. L. Stanfield, T. M. Fieser, R. A. Lerner, I. A. Wilson
Crystal Structures Of An Antibody To A Peptide And Its Complex With Peptide Antigen At 2. 8 A.
Science V. 248 712 1990
PubMed-ID: 2333521
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IGG1-KAPPA B13I2 FAB (LIGHT CHAIN)
    Chains: L, M
    Engineered: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: A/J
 
Molecule 2 - IGG1-KAPPA B13I2 FAB (HEAVY CHAIN)
    Chains: H, J
    Engineered: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: A/J

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : HJLM

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP L:1 , LEU L:3 , ASN L:26 , GLN L:27BINDING SITE FOR RESIDUE NAG L 901

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3J:22 -J:92
4J:142 -J:208
5L:23 -L:88
6L:134 -L:194
7M:23 -M:88
8M:134 -M:194

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Val L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:148 -Pro H:149
5Glu H:150 -Pro H:151
6Thr M:7 -Pro M:8
7Tyr M:140 -Pro M:141
8Phe J:148 -Pro J:149
9Glu J:150 -Pro J:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IGF)

(-) Exons   (0, 0)

(no "Exon" information available for 1IGF)

(-) 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 H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains d1igfh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                         d1igfh2 H:114-227 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1igfH01 H:1-113 Immunoglobulins                                                                                        1igfH02 H:114-226 Immunoglobulins                                                                 - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeee......eeeeee...hhhhheeeeeeee.............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh...eeee...ee....eeeeeeeeee.hhhhhh.eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1igf H    1 EVQLVESGGDLVKPGGSLKLSCAASGFTFSRCAMSWVRQTPEKRLEWVAGISSGGSYTFYPDTVKGRFIISRNNARNTLSLQMSSLRSEDTAIYYCTRYSSDPFYFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVP  227
                                    10        20        30        40        50  |     59        69        79   |||  86        96    || 104       114       124     ||136       146       157|      172       184       194 || || 206|      217     || 
                                                                              52A                            82A||               100B|                           130|                  154|||    169|      180|          196| || 206|            223| 
                                                                                                              82B|                100C                            133                   156||     171       183           198 ||  208             226 
                                                                                                               82C                                                                       157|                               200|                      
                                                                                                                                                                                          162                                202                      


Chain J from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains d1igfj1 J:1-113 Immunoglobulin heavy chain variable domain, VH                                                         d1igfj2 J:114-227 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1igfJ01 J:1-113 Immunoglobulins                                                                                        1igfJ02 J:114-226 Immunoglobulins                                                                 - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee.....eeeeeee......ee........ee..ee....eeeeee...hhhhheeeeeeee.............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh.....ee...ee....eeeeeeeeee........eeeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1igf J    1 EVQLVESGGDLVKPGGSLKLSCAASGFTFSRCAMSWVRQTPEKRLEWVAGISSGGSYTFYPDTVKGRFIISRNNARNTLSLQMSSLRSEDTAIYYCTRYSSDPFYFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVP  227
                                    10        20        30        40        50  |     59        69        79   |||  86        96    || 104       114       124     ||136       146       157|      172       184       194 || || 206|      217     || 
                                                                              52A                            82A||               100B|                           130|                  154|||    169|      180|          196| || 206|            223| 
                                                                                                              82B|                100C                            133                   156||     171       183           198 ||  208             226 
                                                                                                               82C                                                                       157|                               200|                      
                                                                                                                                                                                          162                                202                      


Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d1igfl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1igfl2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1igfL01 L:1-108 Immunoglobulins                                                                                  1igfL02 L:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee...eee..eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1igf L    1 DVLMTQTPLSLPVSLGDQASISCRSNQTILLSDGDTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    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 M from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d1igfm1 M:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1igfm2 M:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1igfM01 M:1-108 Immunoglobulins                                                                                  1igfM02 M:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeee.....eeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1igf M    1 DVLMTQTPLSLPVSLGDQASISCRSNQTILLSDGDTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    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
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 8)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
House mouse (Mus musculus) (616)
1a1igfL02L:109-211
1b1igfL01L:1-108
1c1igfM01M:1-108
1d1igfH02H:114-226
1e1igfJ02J:114-226
1f1igfH01H:1-113
1g1igfJ01J:1-113
1h1igfM02M:109-211

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1IGF)

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 Related Entries

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