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(-) Description

Title :  STRUCTURE OF HYPER-VIL-THAUMATIN
 
Authors :  H. Miyatake, T. Hasegawa, A. Yamano
Date :  08 Dec 05  (Deposition) - 11 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Iodo-Tyrosine, Hydrogen Peroxide Vaporizing Iodine Labeling(Hyper-Vil), Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Miyatake, T. Hasegawa, A. Yamano
New Methods To Prepare Iodinated Derivatives By Vaporizing Iodine Labelling (Vil) And Hydrogen Peroxide Vil (Hyper-Vil)
Acta Crystallogr. , Sect. D V. 62 280 2006
PubMed-ID: 16510975  |  Reference-DOI: 10.1107/S0907444905041909
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THAUMATIN I
    Chains: A
    Organism Common: MIRACLE FRUIT
    Organism Scientific: THAUMATOCOCCUS DANIELLII
    Organism Taxid: 4621

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1IOD5Ligand/IonIODIDE ION
2IYR1Mod. Amino Acid3-IODO-TYROSINE
3TYI4Mod. Amino Acid3,5-DIIODOTYROSINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:93BINDING SITE FOR RESIDUE IOD A 301
2AC2SOFTWAREARG A:125BINDING SITE FOR RESIDUE IOD A 302
3AC3SOFTWAREARG A:175 , IOD A:305BINDING SITE FOR RESIDUE IOD A 304
4AC4SOFTWAREIOD A:304 , IOD A:306BINDING SITE FOR RESIDUE IOD A 305
5AC5SOFTWAREIOD A:305BINDING SITE FOR RESIDUE IOD A 306

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:9 -A:204
2A:56 -A:66
3A:71 -A:77
4A:121 -A:193
5A:126 -A:177
6A:134 -A:145
7A:149 -A:158
8A:159 -A:164

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:83 -Pro A:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D8P)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THAUMATIN_2PS51367 Thaumatin family profile.THM1_THADA1-207  1A:1-207
2THAUMATIN_1PS00316 Thaumatin family signature.THM1_THADA62-77  1A:62-77

(-) Exons   (0, 0)

(no "Exon" information available for 2D8P)

(-) 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:207
 aligned with THM1_THADA | P02883 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
           THM1_THADA     1 ATFEIVNRCSYTVWAAASKGDAALDAGGRQLNSGESWTINVEPGTNGGKIWARTDCYFDDSGSGICKTGDCGGLLRCKRFGRPPTTLAEFSLNQYGKDYIDISNIKGFNVPMNFSPTTRGCRGVRCAADIVGQCPAKLKAPGGGCNDACTVFQTSEYCCTTGKCGPTEYSRFFKRLCPDAFSYVLDKPTTVTCPGSSNYRVTFCPTA 207
               SCOP domains d2d8pa_ A: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains 2d8pA00 A:1-207 Thaumatin                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee....eeeeeeeee....eeeee.......eeeeeeeeeee.....eeeee..................eeeeeeee..eeeeeee........eeeee.......eee..hhhhhhhhhhh.......hhhhhhhhhhhhh.......hhhhhhhhhhh..ee.........eeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) THAUMATIN_2  PDB: A:1-207 UniProt: 1-207                                                                                                                                                                        PROSITE (1)
                PROSITE (2) -------------------------------------------------------------THAUMATIN_1     ---------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d8p A   1 ATFEIVNRCSyTVWAAASKGDAALDAGGRQLNSGESWTINVEPGTNGGKIWARTDCyFDDSGSGICKTGDCGGLLRCKRFGRPPTTLAEFSLNQyGKDyIDISNIKGFNVPMNFSPTTRGCRGVRCAADIVGQCPAKLKAPGGGCNDACTVFQTSEYCCTTGKCGPTEySRFFKRLCPDAFSYVLDKPTTVTCPGSSNYRVTFCPTA 207
                                    10|       20        30        40        50      | 60        70        80        90    |  100       110       120       130       140       150       160       170       180       190       200       
                                     11-TYI                                        57-TYI                                95-TYI                                                                   169-IYR                                  
                                                                                                                             99-TYI
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D8P)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (THM1_THADA | P02883)
cellular component
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.

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    Pro A:83 - Pro A:84   [ RasMol ]  
 

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  2d8p
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  THM1_THADA | P02883
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 Related Entries

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

UniProtKB/Swiss-Prot
        THM1_THADA | P02883: 1kwn 1lr2 1lr3 1lxz 1ly0 1pp3 1rqw 1thi 1thu 1thv 1thw 2a7i 2blr 2blu 2d8o 2g4y 2oqn 2pe7 2vhk 2vhr 2vi1 2vi2 2vi3 2vi4 2vu6 2vu7 2wbz 3al7 3ald 3dzn 3dzp 3dzr 3e0a 3e3s 3n02 3n03 3qy5 3v7v 3v82 3v84 3v87 3v88 3v8a 3vce 3vcg 3vch 3vci 3vcj 3vck 3vhf 3vhg 3vjq 3x3o 3x3p 3x3q 3x3r 3x3s 3x3t 3zej 4axr 4axu 4bal 4bar 4c3c 4dc5 4dc6 4diy 4diz 4dj0 4dj1 4ek0 4eka 4ekb 4ekh 4eko 4ekt 4el2 4el3 4el7 4ela 4tvt 4xvb 4zg3 4zxr 5a47 5amz 5avg 5fgt 5fgx 5jvx 5k7q 5kvw 5kvx 5kvz 5kw0 5kw3 5kw4 5kw5 5kw7 5kw8 5l4r 5lh0 5lh1 5lh3 5lh5 5lh6 5lh7 5lmh 5ln0 5t3g

(-) Related Entries Specified in the PDB File

2d8o 2d8w 2d91 2d97 2d98