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(-) Description

Title :  T. VULCANUS PHYCOCYANIN CRYSTALLIZED IN 2M UREA
 
Authors :  A. Marx, N. Adir
Date :  05 Sep 12  (Deposition) - 06 Mar 13  (Release) - 06 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Photosynthesis, Light Harvesting, Urea Denaturation, Globin-Type, Photosynthetic Antenna, N-Methyl Asparagine, Phycocyanoblilin, Membrane Attached (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Marx, N. Adir
Allophycocyanin And Phycocyanin Crystal Structures Reveal Facets Of Phycobilisome Assembly.
Biochim. Biophys. Acta V. 1827 311 2013
PubMed-ID: 23201474  |  Reference-DOI: 10.1016/J.BBABIO.2012.11.006

(-) Compounds

Molecule 1 - C-PHYCOCYANIN ALPHA SUBUNIT
    Chains: A
    Organism Scientific: THERMOSYNECHOCOCCUS VULCANUS
    Organism Taxid: 32053
    Other Details: CYANOBACTERIUM
    Strain: BP-1
 
Molecule 2 - C-PHYCOCYANIN BETA SUBUNIT
    Chains: B
    Organism Scientific: THERMOSYNECHOCOCCUS VULCANUS
    Organism Taxid: 32053
    Other Details: CYANOBACTERIUM
    Strain: BP-1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 23)

Asymmetric Unit (3, 23)
No.NameCountTypeFull Name
1CYC3Ligand/IonPHYCOCYANOBILIN
2MEN1Mod. Amino AcidN-METHYL ASPARAGINE
3URE19Ligand/IonUREA
Biological Unit 1 (3, 69)
No.NameCountTypeFull Name
1CYC9Ligand/IonPHYCOCYANOBILIN
2MEN3Mod. Amino AcidN-METHYL ASPARAGINE
3URE57Ligand/IonUREA

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:66 , SER A:72 , GLN A:73 , TYR A:74 , ALA A:75 , GLY A:80 , LYS A:83 , CYS A:84 , ARG A:86 , ASP A:87 , TYR A:110 , ILE A:118 , LEU A:124 , TYR A:129 , URE A:209 , URE A:210 , HOH A:301 , HOH A:307 , ARG B:57 , TYR B:76 , THR B:77 , ASN B:78BINDING SITE FOR RESIDUE CYC A 201
02AC2SOFTWARETHR A:3 , PRO A:4 , ILE A:5 , ARG A:30 , ALA A:101 , ASP B:3 , PHE B:5BINDING SITE FOR RESIDUE URE A 202
03AC3SOFTWAREMET A:1 , GLU A:109 , MET B:1BINDING SITE FOR RESIDUE URE A 203
04AC4SOFTWAREGLY A:16 , ARG A:17 , PHE A:18BINDING SITE FOR RESIDUE URE A 204
05AC5SOFTWAREGLU A:131BINDING SITE FOR RESIDUE URE A 207
06AC6SOFTWAREARG A:33 , TYR A:165BINDING SITE FOR RESIDUE URE A 208
07AC7SOFTWAREARG A:86 , CYC A:201 , HOH A:301 , HOH A:314 , ILE B:67 , MET B:81BINDING SITE FOR RESIDUE URE A 209
08AC8SOFTWARETYR A:91 , LEU A:115 , ASN A:119 , TYR A:129 , CYC A:201BINDING SITE FOR RESIDUE URE A 210
09AC9SOFTWAREMEN B:72 , ARG B:79 , ARG B:80 , CYS B:84 , ARG B:86 , ASP B:87 , MET B:88 , ILE B:90 , ARG B:110 , LEU B:122 , THR B:124 , SER B:128 , URE B:208 , HOH B:315BINDING SITE FOR RESIDUE CYC B 201
10BC1SOFTWAREASN A:21 , LEU A:24 , GLN A:25 , ASP A:28 , ASN B:35 , LYS B:36 , ASP B:39 , ASN B:145 , ASP B:146 , ILE B:150 , THR B:151 , PRO B:152 , GLY B:153 , CYS B:155 , MET B:159 , SER B:160 , ALA B:163 , URE B:203 , HOH B:310 , HOH B:329BINDING SITE FOR RESIDUE CYC B 202
11BC2SOFTWARELYS B:32 , GLU B:33 , LYS B:36 , CYC B:202 , HOH B:345BINDING SITE FOR RESIDUE URE B 203
12BC3SOFTWARESER B:156 , ALA B:157 , HOH B:303BINDING SITE FOR RESIDUE URE B 204
13BC4SOFTWAREASP B:39 , GLY B:149 , ILE B:150 , SER B:156 , SER B:160 , HOH B:303 , HOH B:306 , HOH B:310 , HOH B:339BINDING SITE FOR RESIDUE URE B 205
14BC5SOFTWAREMET B:1 , ASP B:109 , ARG B:110BINDING SITE FOR RESIDUE URE B 207
15BC6SOFTWAREARG B:86 , CYC B:201 , HOH B:315BINDING SITE FOR RESIDUE URE B 208
16BC7SOFTWAREALA B:12 , GLU B:17 , PHE B:18 , THR B:20 , GLN B:23 , HOH B:327BINDING SITE FOR RESIDUE URE B 209
17BC8SOFTWAREASP B:138 , ILE B:141 , ALA B:142 , HOH B:319BINDING SITE FOR RESIDUE URE B 210
18BC9SOFTWAREALA B:4 , LYS B:7 , VAL B:8 , HOH B:305BINDING SITE FOR RESIDUE URE B 211
19CC1SOFTWAREASP B:138BINDING SITE FOR RESIDUE URE B 212

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GY3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GY3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GY3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GY3)

(-) Exons   (0, 0)

(no "Exon" information available for 4GY3)

(-) 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:162
                                                                                                                                                                                                  
               SCOP domains d4gy3a_ A: Phycocyanin alpha subunit                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gy3 A   1 MKTPITEAIAAADTQGRFLSNTELQAVDGRFKRAVASMEAARALTNNAQSLIDGAAQAVYQKFPYTTTMQGSQYASTPEGKAKCARDIGYYLRMITYCLVAGGTGPMDEYLIAGLSEINSTFDLSPSWYIEALKYIKANHGLTGQAAVEANAYIDYAINALS 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140|      162       172  
                                                                                                                                                                     140|    150|             
                                                                                                                                                                      143     161             


Chain B from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains d4gy3b_ B: Phycocyanin beta subunit                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gy3 B   1 MLDAFAKVVAQADARGEFLTNAQFDALSNLVKEGNKRLDAVNRITSNASTIVANAARALFAEQPQLIQPGGnAYTNRRMAACLRDMEIILRYVTYAILAGDSSVLDDRCLNGLRETYQALGTPGSSVAVAIQKMKDAAIAIANDPNGITPGDCSALMSEIAGYFDRAAAAVA 174
                                    10        20        30        40        50        60        70 ||     82        92       102       112       122       132       142       152       162       172  
                                                                                                  72-MEN                                                                                                
                                                                                                   75
   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  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GY3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GY3)

(-) Gene Ontology  (4, 8)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        Q71RW8_THEVL | Q71RW8: 1i7y 1on7 3o18 3o2c 4gxe 4n6s
        Q9AM02_THEVL | Q9AM02: 1i7y 1on7 3o18 3o2c 4gxe 4n6s

(-) Related Entries Specified in the PDB File

3o18 SAME PROTEIN IN THE PRESENCE OF 2M UREA
4gxe
4h0m