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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ANTI-STEROID FAB 5F2 IN COMPLEX WITH TESTOSTERONE
 
Authors :  M. H. Niemi, J. Rouvinen
Date :  23 Oct 09  (Deposition) - 26 May 10  (Release) - 07 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Immune System, Antibody, Immunoglobulin Fab Fragment, Anti-Steroid (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. H. Niemi, K. Takkinen, L. K. Amundsen, H. Soderlund, J. Rouvinen, M. Hoyhtya
The Testosterone Binding Mechanism Of An Antibody Derived From A Naive Human Scfv Library
J. Mol. Recognit. V. 24 209 2010
PubMed-ID: 21360611  |  Reference-DOI: 10.1002/JMR.1039

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN LIGHT CHAIN
    ChainsL, A
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainRV308
    Expression System Taxid562
    Expression System VectorPKKTAC
    Expression System Vector TypePLASMID
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - IMMUNOGLOBULIN HEAVY CHAIN
    ChainsH, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainRV308
    Expression System Taxid562
    Expression System VectorPKKTAC
    Expression System Vector TypePLASMID
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABHL
Biological Unit 1 (1x)  HL
Biological Unit 2 (1x)AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1PCA2Mod. Amino AcidPYROGLUTAMIC ACID
2TES2Ligand/IonTESTOSTERONE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1PCA1Mod. Amino AcidPYROGLUTAMIC ACID
2TES1Ligand/IonTESTOSTERONE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1PCA1Mod. Amino AcidPYROGLUTAMIC ACID
2TES1Ligand/IonTESTOSTERONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP H:47 , TYR H:59 , ASP H:99 , TYR H:105 , GLY H:108 , PRO L:99 , TYR L:100BINDING SITE FOR RESIDUE TES H 226
2AC2SOFTWARETRP B:47 , TYR B:59 , ASP B:99 , TYR B:105 , MET B:109BINDING SITE FOR RESIDUE TES B 226

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:90
2A:138 -A:198
3B:22 -B:96
4B:149 -B:205
5H:22 -H:96
6H:149 -H:205
7L:22 -L:90
8L:138 -L:198

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Tyr L:144 -Pro L:145
2Phe H:155 -Pro H:156
3Glu H:157 -Pro H:158
4Tyr A:144 -Pro A:145
5Phe B:155 -Pro B:156
6Glu B:157 -Pro B:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KDM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KDM)

(-) Exons   (0, 0)

(no "Exon" information available for 3KDM)

(-) 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 d3kdma1 A:3-111 automated matches                                                                            d3kdma2 A:112-218 automated matches                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------3kdmA02 A:113-218 Immunoglobulins                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee.....eeeeee...........eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeee......eee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kdm A   3 ALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYGVTNRPSGVSNRFSGSKSGNTASLTISGLQAGDEADYYCSSYTSTRTPYVFGTGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 218
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      

Chain B from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3kdmB01 B:2-122 Immunoglobulins                                                                                          3kdmB02 B:123-222 Immunoglobulins                                                                   - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee......eeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeee......eeeeee...hhhhheeeeeeee...........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh...eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kdm B   1 xVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDPGLWDYYYGMDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSSVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPK 223
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
                            1-PCA                                                                                                                                                                                                                          

Chain H from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3kdmH01 H:2-122 Immunoglobulins                                                                                          3kdmH02 H:123-222 Immunoglobulins                                                                   - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eeehhhhhh.eeeeee....eeeeee...hhhhheeeeeee............ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh...eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kdm H   1 xVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDPGLWDYYYGMDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSSVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPK 223
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
                            1-PCA                                                                                                                                                                                                                          

Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d3kdml1 L:3-111 automated matches                                                                            d3kdml2 L:112-218 automated matches                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------3kdmL02 L:113-218 Immunoglobulins                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee.....eeeeee...........eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeee......eee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kdm L   3 ALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYGVTNRPSGVSNRFSGSKSGNTASLTISGLQAGDEADYYCSSYTSTRTPYVFGTGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 218
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3KDM)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3KDM)

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