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(-) Description

Title :  CRYSTAL STRUCTURE OF CYTOKININ-SPECIFIC BINDING PROTEIN IN COMPLEX WITH CYTOKININ AND TA6BR12
 
Authors :  O. Pasternak, A. Bujacz, J. Biesiadka, G. Bujacz, M. Sikorski, M. Jasko
Date :  21 Jan 08  (Deposition) - 20 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  B,C  (1x)
Biol. Unit 6:  A  (1x)
Biol. Unit 7:  D  (1x)
Keywords :  Mad, Ta6Br12 Complex, Cytokinins, Zeatin, Pathogenesis-Related Proteins, Plant Defense, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Pasternak, A. Bujacz, J. Biesiadka, G. Bujacz, M. Sikorski, M. Jaskolski
Mad Phasing Using The (Ta(6)Br(12))(2+) Cluster: A Retrospective Study
Acta Crystallogr. , Sect. D V. 64 595 2008
PubMed-ID: 18453695  |  Reference-DOI: 10.1107/S0907444908007853
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOKININ-SPECIFIC BINDING PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-3A
    Expression System Strain: BL21
    Expression System Vector Type: PLASMID
    Gene: VRCSBP
    Organism Scientific: VIGNA RADIATA

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x):  BC 
Biological Unit 6 (1x): A   
Biological Unit 7 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2NA2Ligand/IonSODIUM ION
3TBR5Ligand/IonHEXATANTALUM DODECABROMIDE
4ZEA6Ligand/Ion(2E)-2-METHYL-4-(9H-PURIN-6-YLAMINO)BUT-2-EN-1-OL
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2NA-1Ligand/IonSODIUM ION
3TBR2Ligand/IonHEXATANTALUM DODECABROMIDE
4ZEA2Ligand/Ion(2E)-2-METHYL-4-(9H-PURIN-6-YLAMINO)BUT-2-EN-1-OL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2NA-1Ligand/IonSODIUM ION
3TBR-1Ligand/IonHEXATANTALUM DODECABROMIDE
4ZEA2Ligand/Ion(2E)-2-METHYL-4-(9H-PURIN-6-YLAMINO)BUT-2-EN-1-OL
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2NA-1Ligand/IonSODIUM ION
3TBR2Ligand/IonHEXATANTALUM DODECABROMIDE
4ZEA-1Ligand/Ion(2E)-2-METHYL-4-(9H-PURIN-6-YLAMINO)BUT-2-EN-1-OL
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2NA-1Ligand/IonSODIUM ION
3TBR1Ligand/IonHEXATANTALUM DODECABROMIDE
4ZEA2Ligand/Ion(2E)-2-METHYL-4-(9H-PURIN-6-YLAMINO)BUT-2-EN-1-OL
Biological Unit 5 (2, 4)
No.NameCountTypeFull Name
1EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2NA-1Ligand/IonSODIUM ION
3TBR2Ligand/IonHEXATANTALUM DODECABROMIDE
4ZEA2Ligand/Ion(2E)-2-METHYL-4-(9H-PURIN-6-YLAMINO)BUT-2-EN-1-OL
Biological Unit 6 (3, 5)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2NA-1Ligand/IonSODIUM ION
3TBR2Ligand/IonHEXATANTALUM DODECABROMIDE
4ZEA2Ligand/Ion(2E)-2-METHYL-4-(9H-PURIN-6-YLAMINO)BUT-2-EN-1-OL
Biological Unit 7 (2, 3)
No.NameCountTypeFull Name
1EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2NA-1Ligand/IonSODIUM ION
3TBR1Ligand/IonHEXATANTALUM DODECABROMIDE
4ZEA2Ligand/Ion(2E)-2-METHYL-4-(9H-PURIN-6-YLAMINO)BUT-2-EN-1-OL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP B:123 , ILE B:126 , HOH B:172 , HOH B:208 , HOH B:255 , HOH B:256BINDING SITE FOR RESIDUE NA B 156
02AC2SOFTWARESER C:124 , ILE C:126 , HOH C:203 , HOH C:243 , HOH C:272 , HOH C:314BINDING SITE FOR RESIDUE NA C 156
03AC3SOFTWARELEU A:22 , PHE A:26 , GLU A:69 , THR A:139 , TYR A:142 , ZEA A:157 , HOH A:179 , HOH A:241BINDING SITE FOR RESIDUE ZEA A 156
04AC4SOFTWARELEU A:34 , ILE A:37 , PHE A:58 , VAL A:62 , GLN A:67 , GLY A:89 , TYR A:90 , GLN A:93 , ZEA A:156 , HOH A:240 , HOH A:241 , HOH A:244 , TBR D:158BINDING SITE FOR RESIDUE ZEA A 157
05AC5SOFTWARELEU B:22 , PHE B:26 , GLN B:67 , GLU B:69 , THR B:100 , THR B:139 , TYR B:142 , ZEA B:158 , HOH B:163BINDING SITE FOR RESIDUE ZEA B 157
06AC6SOFTWAREPHE B:56 , GLN B:67 , GLU B:69 , TYR B:90 , ZEA B:157 , HOH B:261 , HOH B:262 , HOH B:284BINDING SITE FOR RESIDUE ZEA B 158
07AC7SOFTWARELEU D:22 , PHE D:56 , GLN D:67 , GLU D:69 , THR D:139 , TYR D:142 , ZEA D:157 , HOH D:231BINDING SITE FOR RESIDUE ZEA D 156
08AC8SOFTWARELEU D:34 , PHE D:56 , PRO D:64 , GLN D:67 , GLY D:89 , TYR D:90 , GLN D:93 , ZEA D:156 , HOH D:255BINDING SITE FOR RESIDUE ZEA D 157
09AC9SOFTWAREASP A:40 , GLN A:42 , ASN A:57 , TBR A:159 , HOH A:277 , HOH A:278 , ARG B:14 , ASP D:125 , ILE D:126 , GLU D:127BINDING SITE FOR RESIDUE TBR A 158
10BC1SOFTWARESER B:124 , ILE B:126 , GLU B:127 , HOH B:305 , LYS C:39 , ASP C:40 , GLN C:42 , HOH C:266 , ARG D:14BINDING SITE FOR RESIDUE TBR C 157
11BC2SOFTWARELYS A:39 , TBR A:158 , HOH A:250 , HOH A:278 , SER B:151 , MET D:1BINDING SITE FOR RESIDUE TBR A 159
12BC3SOFTWARELYS A:129 , ZEA A:157 , ASP D:75 , SER D:78 , GLU D:80 , HOH D:248BINDING SITE FOR RESIDUE TBR D 158
13BC4SOFTWAREILE C:37 , GLU C:73 , ASP C:75 , SER C:78 , GLU C:80 , LYS C:134 , SER C:138 , HOH C:251 , HOH C:257 , HOH C:264 , HOH C:265 , HOH C:297BINDING SITE FOR RESIDUE TBR C 158
14BC5SOFTWAREASP A:47 , GLY A:49 , PHE A:74 , ASP A:75 , GLU A:76 , HOH A:187 , HOH A:220 , HOH A:264 , THR B:133 , HOH B:236BINDING SITE FOR RESIDUE EPE A 160

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C0V)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:63 -Pro A:64
2Ser B:63 -Pro B:64
3Ser C:63 -Pro C:64
4Ser D:63 -Pro D:64

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C0V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C0V)

(-) Exons   (0, 0)

(no "Exon" information available for 3C0V)

(-) 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:151
 aligned with Q9ZWP8_VIGRA | Q9ZWP8 from UniProtKB/TrEMBL  Length:155

    Alignment length:151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 
         Q9ZWP8_VIGRA     1 MVKEFNTQTELSVRLEALWAVLSKDFITVVPKVLPHIVKDVQLIEGDGGVGTILIFNFLPEVSPSYQREEITEFDESSHEIGLQVIEGGYLNQGLSYYKTTFKLSEIEEDKTLVNVKISYDHDSDIEEKVTPTKTSQSTLMYLRRLERYLS 151
               SCOP domains d3c0va_ A: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee..hhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......eeeeee.......eeeeeeeeee....eeeeeeeee.hhhh...eeeeeeeeeeee..eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c0v A   1 MVKEFNTQTELSVRLEALWAVLSKDFITVVPKVLPHIVKDVQLIEGDGGVGTILIFNFLPEVSPSYQREEITEFDESSHEIGLQVIEGGYLSQGLSYYKTTFKLSEIEEDKTLVNVKISYDHDSDIEEKVTPTKTSQSTLMYLRRLERYLS 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 


Chain B from PDB  Type:PROTEIN  Length:151
 aligned with Q9ZWP8_VIGRA | Q9ZWP8 from UniProtKB/TrEMBL  Length:155

    Alignment length:151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 
         Q9ZWP8_VIGRA     1 MVKEFNTQTELSVRLEALWAVLSKDFITVVPKVLPHIVKDVQLIEGDGGVGTILIFNFLPEVSPSYQREEITEFDESSHEIGLQVIEGGYLNQGLSYYKTTFKLSEIEEDKTLVNVKISYDHDSDIEEKVTPTKTSQSTLMYLRRLERYLS 151
               SCOP domains d3c0vb_ B: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee..hhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......eeeeee.......eeeeeeeeee....eeeeeeeee.hhhh.eeeeeeeeeeeeee..eeeeeeeeeeee........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c0v B   1 MVKEFNTQTELSVRLEALWAVLSKDFITVVPKVLPHIVKDVQLIEGDGGVGTILIFNFLPEVSPSYQREEITEFDESSHEIGLQVIEGGYLSQGLSYYKTTFKLSEIEEDKTLVNVKISYDHDSDIEEKVTPTKTSQSTLMYLRRLERYLS 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 


Chain C from PDB  Type:PROTEIN  Length:151
 aligned with Q9ZWP8_VIGRA | Q9ZWP8 from UniProtKB/TrEMBL  Length:155

    Alignment length:151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 
         Q9ZWP8_VIGRA     1 MVKEFNTQTELSVRLEALWAVLSKDFITVVPKVLPHIVKDVQLIEGDGGVGTILIFNFLPEVSPSYQREEITEFDESSHEIGLQVIEGGYLNQGLSYYKTTFKLSEIEEDKTLVNVKISYDHDSDIEEKVTPTKTSQSTLMYLRRLERYLS 151
               SCOP domains d3c0vc_ C: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee..hhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......eeeeee.......eeeeeeeeee....eeeeeeeee.hhhh.eeeeeeeeeeeeee..eeeeeeeeeeee........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c0v C   1 MVKEFNTQTELSVRLEALWAVLSKDFITVVPKVLPHIVKDVQLIEGDGGVGTILIFNFLPEVSPSYQREEITEFDESSHEIGLQVIEGGYLSQGLSYYKTTFKLSEIEEDKTLVNVKISYDHDSDIEEKVTPTKTSQSTLMYLRRLERYLS 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 


Chain D from PDB  Type:PROTEIN  Length:152
 aligned with Q9ZWP8_VIGRA | Q9ZWP8 from UniProtKB/TrEMBL  Length:155

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
         Q9ZWP8_VIGRA     1 MVKEFNTQTELSVRLEALWAVLSKDFITVVPKVLPHIVKDVQLIEGDGGVGTILIFNFLPEVSPSYQREEITEFDESSHEIGLQVIEGGYLNQGLSYYKTTFKLSEIEEDKTLVNVKISYDHDSDIEEKVTPTKTSQSTLMYLRRLERYLSN 152
               SCOP domains d3c0vd_ D: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee..hhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......eeeeee.......eeeeeeeeee....eeeeeeeee.hhhh.eeeeeeeeeeeeee..eeeeeeeeeeee........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c0v D   1 MVKEFNTQTELSVRLEALWAVLSKDFITVVPKVLPHIVKDVQLIEGDGGVGTILIFNFLPEVSPSYQREEITEFDESSHEIGLQVIEGGYLSQGLSYYKTTFKLSEIEEDKTLVNVKISYDHDSDIEEKVTPTKTSQSTLMYLRRLERYLSN 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   Legend:   → Mismatch (orange background)
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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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3C0V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C0V)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9ZWP8_VIGRA | Q9ZWP8)
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0009607    response to biotic stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism.

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  3c0v
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  Q9ZWP8_VIGRA | Q9ZWP8
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 Related Entries

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

UniProtKB/TrEMBL
        Q9ZWP8_VIGRA | Q9ZWP8: 2flh 4psb

(-) Related Entries Specified in the PDB File

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