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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FAB M75
 
Authors :  V. Kral, P. Mader, R. Stouracova, M. Fabry, J. Sedlacek, J. Brynda
Date :  04 Jul 06  (Deposition) - 13 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin, Fab Fragment, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Kral, P. Mader, R. Collard, M. Fabry, M. Horejsi, P. Rezacova, M. Kozisek, J. Zavada, J. Sedlacek, L. Rulisek, J. Brynda
Stabilization Of Antibody Structure Upon Association To A Human Carbonic Anhydrase Ix Epitope Studied By X-Ray Crystallography, Microcalorimetry, And Molecular Dynamics Simulations.
Proteins V. 71 1275 2008
PubMed-ID: 18041760  |  Reference-DOI: 10.1002/PROT.21821

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN LIGHT CHAIN FAB FRAGMENT
    Cell: HYBRIDOMA CELLS
    Chains: L
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - IMMUNOGLOBULIN HEAVY CHAIN FAB FRAGMENT
    Cell: HYBRIDOMA CELLS
    Chains: H
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU H:11 , ALA H:120 , LYS H:121 , THR H:122 , PRO H:153BINDING SITE FOR RESIDUE GOL H 219

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:98
2H:146 -H:201
3L:23 -L:93
4L:139 -L:199
5L:219 -H:134

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Val L:99 -Pro L:100
3Tyr L:145 -Pro L:146
4Pro H:132 -Gly H:133
5Phe H:152 -Pro H:153
6Trp H:194 -Pro H:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2HKH)

(-) 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:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2hkhH01 H:2-119 Immunoglobulins                                                                                       2hkhH02 H:120-218 Immunoglobulins                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eee.....eeeeee..........eeeeee.....eeeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeee.......ee...eeeee........eeeee.......eeeeeeeeeee.....eeeee..eeeeeeeee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hkh H   2 VQVVESGGGLVQPKGSLKLSCVVSGSTLNNYAMNWVRQAPGKGLEWVARIRSKSNNYATYYADSVKDRFTISRDDSQSMIYLQMNNLKTEDTAMYYCVTYGNHPFAYWGQGTLVTVSAAKTTPPSVYPLAPGCTGSSVTLGCLVKGYFPESVTVTWNSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEP 218
                                    11        21        31        41        51        61        71        81        91       101       111       121       131  ||   144       154      |169       179       189       199       209         
                                                                                                                                                              134|                    161|                                                   
                                                                                                                                                               138                     167                                                   


Chain L from PDB  Type:PROTEIN  Length:219
 aligned with KV2A7_MOUSE | P01631 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:219
                                                                                                                                          113                                                                                                          
                                    10        20        30        40        50        60        70        80        90       100       110  |      -         -         -         -         -         -         -         -         -         -         
          KV2A7_MOUSE     1 DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLNWYLQKAGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGIYFCSQTTHVPPTFGGGTKLEIKR----------------------------------------------------------------------------------------------------------   -
               SCOP domains d2hkhl1 L:1-112 automated matches                                                                               d2hkhl2 L:113-219 automated matches                                                                         SCOP domains
               CATH domains 2hkhL01 L:1-113 Immunoglobulins                                                                                  2hkhL02 L:114-216 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.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hkh L   1 DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPNLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (2, 2)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain L   (KV2A7_MOUSE | P01631)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

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  Cis Peptide Bonds
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    Val L:99 - Pro L:100   [ RasMol ]  
 

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  2hkh
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  KV2A7_MOUSE | P01631
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 Related Entries

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

UniProtKB/Swiss-Prot
        KV2A7_MOUSE | P01631: 1bfv 1cfv 1dlf 1maj 1mak 1n4x 1svz 1wz1 2bfv 2dlf 2hkf 2ipt 2iqa 2o5x 2o5y 2o5z 2r0w 2vq1

(-) Related Entries Specified in the PDB File

2hkf