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(-) Description

Title :  FLUOROGEN ACTIVATING PROTEIN M8VLA4(S55P) IN COMPLEX WITH DIMETHYLINDOLE RED
 
Authors :  R. Stanfield, N. Senutovitch, S. Bhattacharyya, G. Rule, I. A. Wilson, B. Armitage, A. S. Waggoner, P. Berget
Date :  20 Jul 11  (Deposition) - 21 Mar 12  (Release) - 11 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Immunoglobulin Fold, Fluorogen Activation, Dimethylindole Red, Dye- Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Senutovitch, R. L. Stanfield, S. Bhattacharyya, G. S. Rule, I. A. Wilson, B. A. Armitage, A. S. Waggoner, P. B. Berget
A Variable Light Domain Fluorogen Activating Protein Homodimerizes To Activate Dimethylindole Red.
Biochemistry V. 51 2471 2012
PubMed-ID: 22390683  |  Reference-DOI: 10.1021/BI201422G

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN VARIABLE LAMBDA DOMAIN M8VLA4(S55P)
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAK400
    Expression System Strain: MACHTI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1DIW1Ligand/Ion1-(3-SULFOPROPYL)-4-[(1E,3E)-3-(1,3,3-TRIMETHYL-1,3-DIHYDRO-2H-INDOL-2-YLIDENE)PROP-1-EN-1-YL]QUINOLINIUM
2EDO7Ligand/Ion1,2-ETHANEDIOL
3PCA2Mod. Amino AcidPYROGLUTAMIC ACID
4SO41Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:34 , TYR A:49 , ARG A:53 , PRO A:55 , SER A:56 , LEU A:89 , TRP A:96 , HOH A:317 , TYR B:34 , TYR B:49 , PRO B:55 , SER B:56 , TRP B:96 , SO4 B:201BINDING SITE FOR RESIDUE DIW A 201
2AC2SOFTWARESER A:63 , GLY A:64 , SER A:65 , SER A:72 , ALA A:74 , HOH B:340BINDING SITE FOR RESIDUE EDO A 202
3AC3SOFTWAREGLN A:37 , LYS A:45 , PRO A:59 , ARG A:61 , PHE A:62 , GLU A:81 , ASP A:82BINDING SITE FOR RESIDUE EDO A 203
4AC4SOFTWARESER A:65 , LYS A:66 , SER A:67 , SER A:70 , ALA A:71 , SER A:72 , THR B:5 , SER B:24 , SER B:94BINDING SITE FOR RESIDUE EDO A 204
5AC5SOFTWAREGLN A:38 , PRO A:40 , ASP A:85 , HOH A:306 , HOH A:380BINDING SITE FOR RESIDUE EDO A 205
6AC6SOFTWAREPHE B:22 , SER B:65 , LYS B:66 , SER B:70 , SER B:72BINDING SITE FOR RESIDUE EDO A 206
7AC7SOFTWARESER A:80 , HOH A:325BINDING SITE FOR RESIDUE EDO A 207
8AC8SOFTWARETYR A:36 , TYR A:87 , PHE A:98 , HOH A:321 , HOH A:339BINDING SITE FOR RESIDUE EDO A 208
9AC9SOFTWAREPRO A:55 , DIW A:201 , ASN B:50 , HOH B:309 , HOH B:311 , HOH B:326BINDING SITE FOR RESIDUE SO4 B 201

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2B:23 -B:88

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3T0X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T0X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3T0X)

(-) Exons   (0, 0)

(no "Exon" information available for 3T0X)

(-) 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 A from PDB  Type:PROTEIN  Length:111
                                                                                                                                                
               SCOP domains d3t0xa_ A: automated matches                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee....eeeeeee..........eeeeee......eeee.............eeeeee..eeeeeee..hhhhheeeeeeeee.................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                3t0x A    1 xPVLTQSPSVSGTPGQKVTIFCSGSSSNVEDNSVYWYQQFPGTTPKVLIYNDDRRPSGVPDRFSGSKSGTSASLAISGLRSEDEADYYCLSWDDSLNGWVFGGGTKVTVLD  107
                            |       11        21      ||29        39        49        59        69        79        89      ||97      106A 
                            |       9|              27A|                                                                  95A|        106A 
                            1-PCA   11               27B                                                                   95B             


Chain B from PDB  Type:PROTEIN  Length:109
                                                                                                                                              
               SCOP domains d3t0xb_ B: automated matches                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee......eeeeee...........eeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeeee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                3t0x B    1 xPVLTQSPSVSGTPGQKVTIFCSGSSSNVEDNSVYWYQQFPGTTPKVLIYNDDRRPSGVPDRFSGSKSGTSASLAISGLRSEDEADYYCLSWDDSLNGWVFGGGTKVTV  106
                            |       11        21      ||29        39        49        59        69        79        89      ||97         
                            |       9|              27A|                                                                  95A|           
                            1-PCA   11               27B                                                                   95B
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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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T0X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T0X)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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 Related Entries

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(-) Related Entries Specified in the PDB File

3t0v 3t0w