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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE ANTI-TESTOSTERONE FAB IN COMPLEX WITH TESTOSTERONE
 
Authors :  J. M. Valjakka, A. Hemminki, S. Niemi, H. Soderlund, K. Takkinen, J. Rouvinen
Date :  15 Nov 04  (Deposition) - 23 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  H,L  (2x)
Keywords :  Fab Fragment, Anti-Steroid, Testosterone Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Valjakka, A. Hemminki, S. Niemi, H. Soderlund, K. Takkinen, J. Rouvinen
Crystal Structure Of An In Vitro Affinity- And Specificity-Matured Anti-Testosterone Fab In Complex With Testosterone. Improved Affinity Results From Small Structural Changes Within The Variable Domains
J. Biol. Chem. V. 277 44021 2002
PubMed-ID: 12196551  |  Reference-DOI: 10.1074/JBC.M208392200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTI-TESTOSTERONE (LIGHT CHAIN)
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKKTAC
    Expression System Strain: RV308
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: FAB77 FRAGMENT
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - ANTI-TESTOSTERONE (HEAVY CHAIN)
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKKTAC
    Expression System Strain: RV308
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: FAB77 FRAGMENT
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : HL
Biological Unit 1 (1x): HL
Biological Unit 2 (2x): HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1TES1Ligand/IonTESTOSTERONE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1TES1Ligand/IonTESTOSTERONE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1TES2Ligand/IonTESTOSTERONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER H:35 , SER H:50 , TYR H:58 , ALA H:98 , TYR H:102 , GLY H:104 , LEU H:105 , HOH H:749 , ARG L:32 , PHE L:94 , GLY L:96 , VAL L:99 , ASP L:189BINDING SITE FOR RESIDUE TES H 1010

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1H:22 -H:95
2H:145 -H:200
3L:23 -L:93
4L:139 -L:199
5L:219 -H:220

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Thr L:7 -Pro L:8
2Val L:99 -Pro L:100
3Tyr L:145 -Pro L:146
4Phe H:151 -Pro H:152
5Glu H:153 -Pro H:154
6Trp H:193 -Pro H:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VPO)

(-) 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 d1vpoh1 H:1-118 Immunoglobulin heavy chain variable domain, VH                                                        d1vpoh2 H:119-221 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                         SCOP domains
               CATH domains 1vpoH01 H:1-118 Immunoglobulins                                                                                       1vpoH02 H:119-217 Immunoglobulins                                                                  ---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee.....eeeeeee.....eee........eeeee....eeeeee...hhhhheeeeeeeeee..eeee.....eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.hhh.....eeeeeehhhheeeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vpo H   1 EVKLVESGGGLVKPGGSLKLSCAASGFTFSRYALSWVRQTADKRLEWVASIVSGGNTYYSGSVKGRFTISRDIARNILYLQMSSLRSEDTAMYYCARAYYGYVGLVHWGQGTLVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCG 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 


Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d1vpol1 L:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1vpol2 L:113-219 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1vpoL01 L:1-113 Immunoglobulins                                                                                  1vpoL02 L:114-216 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vpo L   1 DVVVTQTPLSLPVSLGDQASISCRSSEVIVTRNGYTPIEWYLQKPGQSPKLLIYKAYKRFPGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFDGSTVPPKFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRDEC 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
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  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 1VPO)

(-) Gene Ontology  (0, 0)

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

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  1vpo
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(-) Related Entries Specified in the PDB File

1l7t CRYSTAL STRUCTURE ANALYSIS OF THE ANTI-TESTOSTERONE FAB FRAGMENT