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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. Unit :  H,L,P
Biol. Unit 1:  H,L,P  (1x)
Biol. Unit 2:  H,L,P  (2x)
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
    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
    Engineered: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: A/J
 
Molecule 3 - PEPTIDE (RESIDUES 69-87 OF MYOHEMERYTHRIN)
    Chains: P
    Engineered: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : HLP
Biological Unit 1 (1x): HLP
Biological Unit 2 (2x): HLP

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU L:3 , ASN L:26 , GLN L:27BINDING SITE FOR RESIDUE NAG L 600

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (4, 4)

Asymmetric 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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2IGF)

(-) 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 H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains d2igfh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                         d2igfh2 H:114-233 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 2igfH01 H:1-113 Immunoglobulins                                                                                        2igfH02 H:114-226 Immunoglobulins                                                                 ---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeee....eeeeee...hhhhheeeeeeee.............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh.....ee...ee....eeeeeeeeee........eeeeee.hhhh.eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2igf H    1 EVQLVESGGDLVKPGGSLKLSCAASGFTFSRCAMSWVRQTPEKRLEWVAGISSGGSYTFYPDTVKGRFIISRNNARNTLSLQMSSLRSEDTAIYYCTRYSSDPFYFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC  233
                                    10        20        30        40        50  |     59        69        79   |||  86        96    || 104       114       124     ||136       146       157|      172       184       194 || || 206|      217     ||232 
                                                                              52A                            82A||               100B|                           130|                  154|||    169|      180|          196| || 206|            223| || 
                                                                                                              82B|                100C                            133                   156||     171       183           198 ||  208             226 || 
                                                                                                               82C                                                                       157|                               200|                    228| 
                                                                                                                                                                                          162                                202                     232 


Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d2igfl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d2igfl2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 2igfL01 L:1-108 Immunoglobulins                                                                                  2igfL02 L:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee....eeeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeee.......eeeeee........eeeee...........eeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2igf 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 P from PDB  Type:PROTEIN  Length:7
 aligned with HEMTM_THEHE | P02247 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:7
         HEMTM_THEHE     69 EVVPHKK   75
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                2igf P   69 EVVPHKK   75
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain P   (HEMTM_THEHE | P02247)
molecular function
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005344    oxygen transporter activity    Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
    GO:0015671    oxygen transport    The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HEMTM_THEHE | P02247: 1a7d 1a7e 2mhr

(-) Related Entries Specified in the PDB File

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