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(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURE OF PHYCOERYTHRIN 545 FROM THE MARINE CRYPTOPHYTE RHODOMONAS CS24
 
Authors :  A. B. Doust, C. N. J. Marai, S. J. Harrop, K. E. Wilk, P. M. G. Curmi, G. D. Scholes
Date :  16 Sep 04  (Deposition) - 30 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.97
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Phycoerythrin, Light-Harvesting Protein, Cryptophyte, Photosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. B. Doust, C. N. J. Marai, S. J. Harrop, K. E. Wilk, P. M. G. Curmi, G. D. Scholes
Developing A Structure-Function Model For The Cryptophyte Phycoerythrin 545 Using Ultrahigh Resolution Crystallography And Ultrafast Laser Spectroscopy
J. Mol. Biol. V. 344 135 2004
PubMed-ID: 15504407  |  Reference-DOI: 10.1016/J.JMB.2004.09.044
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHYCOERYTHRIN ALPHA-3 CHAIN
    ChainsA
    Organism ScientificRHODOMONAS SP. CS24
    Organism Taxid79257
    StrainCS 24
    SynonymCRYPTOPHYTAN PHYCOERYTHRIN (ALPHA-1 CHAIN)
 
Molecule 2 - PHYCOERYTHRIN ALPHA-2 CHAIN
    ChainsB
    Organism ScientificRHODOMONAS SP. CS24
    Organism Taxid79257
    StrainCS 24
    SynonymCRYPTOPHYTAN PHYCOERYTHRIN (ALPHA-2 CHAIN)
 
Molecule 3 - B-PHYCOERYTHRIN BETA CHAIN
    ChainsC, D
    Organism ScientificRHODOMONAS SP. CS24
    Organism Taxid79257
    StrainCS 24
    SynonymCRYPTOPHYTAN PHYCOERYTHRIN (BETA CHAIN)

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 14)

Asymmetric/Biological Unit (6, 14)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2DBV2Ligand/Ion15,16-DIHYDROBILIVERDIN
3LYZ1Mod. Amino Acid5-HYDROXYLYSINE
4MEN2Mod. Amino AcidN-METHYL ASPARAGINE
5MG2Ligand/IonMAGNESIUM ION
6PEB6Ligand/IonPHYCOERYTHROBILIN

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:68 , SER C:147 , GLN C:148 , PEB D:250 , HOH D:2083BINDING SITE FOR RESIDUE CL C 3001
02AC2SOFTWAREHOH A:2002 , HOH A:2003 , HOH B:1041 , HOH B:1042 , HOH B:1043 , HOH D:2003BINDING SITE FOR RESIDUE MG A 2001
03AC3SOFTWAREHOH D:2004 , HOH D:2005 , HOH D:2006 , HOH D:2007 , HOH D:2008 , HOH D:2009BINDING SITE FOR RESIDUE MG D 2002
04AC4SOFTWAREPHE A:14 , CYS A:19 , SER A:20 , ARG A:21 , PRO A:23 , LYS A:24 , GLU A:25 , SER A:26 , ASP A:36 , GLU A:37 , MET A:38 , MET A:39 , LYS A:41 , HOH A:2005 , HOH A:2009 , HOH A:2018 , HOH A:2020 , HOH A:2026 , HOH A:2031 , HOH A:2078 , HOH A:2197 , LEU B:62 , MET B:65 , THR B:66 , TYR C:18 , PRO D:64 , SER D:65 , ILE D:67 , SER D:68BINDING SITE FOR RESIDUE DBV A 219
05AC5SOFTWAREPHE A:64 , ASN A:76 , PHE B:14 , CYS B:19 , SER B:20 , ARG B:21 , PRO B:23 , LYS B:24 , GLU B:25 , TYR B:26 , ASP B:36 , GLU B:37 , MET B:38 , MET B:39 , LYS B:41 , HOH B:1046 , HOH B:1047 , HOH B:1051 , HOH B:1065 , HOH B:1079 , HOH B:1080 , HOH B:1085 , HOH B:1087 , HOH B:1105 , SER C:65 , ILE C:67 , SER C:68BINDING SITE FOR RESIDUE DBV B 219
06AC6SOFTWAREPHE A:64 , GLU A:65 , LYS A:66 , ASP A:69 , PRO A:71 , PHE A:72 , THR A:73 , SER A:74 , CYS C:50 , ASP C:54 , SER C:57 , GLY C:58 , CYS C:61 , ARG C:129 , ALA C:136 , CYS C:137 , PHE C:141 , ALA C:146 , SER C:147 , GLN C:148 , HOH C:3006 , HOH C:3036 , HOH C:3043 , HOH C:3046 , HOH C:3139 , HOH C:3281 , HOH C:3286 , HOH C:3292 , LYS D:29 , HOH D:2028BINDING SITE FOR RESIDUE PEB C 250
07AC7SOFTWAREILE A:13 , ARG A:17 , GLN A:34 , MET A:38 , MET A:39 , LYS C:28 , ASN C:35 , LYS C:36 , LEU C:38 , ASP C:39 , SER C:40 , VAL C:142 , ASN C:143 , ASN C:144 , THR C:153 , PRO C:154 , GLN C:155 , GLY C:156 , CYS C:158 , HOH C:3009 , HOH C:3037 , HOH C:3060 , HOH C:3085 , HOH C:3115 , HOH C:3128 , HOH C:3170 , HOH C:3250BINDING SITE FOR RESIDUE PEB C 258
08AC8SOFTWAREMET A:2 , LYZ A:4 , SER A:5 , ALA A:6 , MET C:59 , MEN C:72 , CYS C:73 , ARG C:77 , ARG C:78 , ALA C:81 , CYS C:82 , ARG C:84 , ASP C:85 , ILE C:88 , ARG C:108 , LEU C:120 , VAL C:122 , ASN C:127 , HOH C:3022 , HOH C:3033 , HOH C:3045 , HOH C:3061 , HOH C:3087 , HOH C:3219BINDING SITE FOR RESIDUE PEB C 282
09AC9SOFTWAREGLY A:67 , ILE A:68 , LYS B:64 , GLN C:148 , CL C:3001 , ASN D:47 , CYS D:50 , ASP D:54 , SER D:57 , GLY D:58 , CYS D:61 , ARG D:129 , ALA D:136 , CYS D:137 , HOH D:2026 , HOH D:2071 , HOH D:2072 , HOH D:2116 , HOH D:2120 , HOH D:2162 , HOH D:2234 , HOH D:2289 , HOH D:2309 , HOH D:2359 , HOH D:2371BINDING SITE FOR RESIDUE PEB D 250
10BC1SOFTWAREILE B:13 , ASP B:15 , ARG B:17 , LYS B:34 , MET B:38 , LYS D:28 , ASN D:35 , LYS D:36 , LEU D:38 , ASP D:39 , SER D:40 , VAL D:142 , LEU D:151 , THR D:153 , PRO D:154 , GLN D:155 , GLY D:156 , CYS D:158 , HOH D:2033 , HOH D:2056 , HOH D:2058 , HOH D:2060 , HOH D:2068 , HOH D:2088 , HOH D:2102 , HOH D:2104 , HOH D:2246BINDING SITE FOR RESIDUE PEB D 258
11BC2SOFTWAREMET B:2 , LYS B:4 , SER B:5 , ALA B:6 , MEN D:72 , CYS D:73 , ARG D:77 , ARG D:78 , ALA D:81 , CYS D:82 , ARG D:84 , ASP D:85 , ILE D:88 , ARG D:108 , LEU D:120 , VAL D:122 , ASN D:127 , HOH D:2067 , HOH D:2093 , HOH D:2108 , HOH D:2173 , HOH D:2191 , HOH D:2194 , HOH D:2364BINDING SITE FOR RESIDUE PEB D 282

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XG0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XG0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XG0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XG0)

(-) Exons   (0, 0)

(no "Exon" information available for 1XG0)

(-) 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:76
 aligned with PHE3_RHDS2 | Q00433 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:76
                                    62        72        82        92       102       112       122      
           PHE3_RHDS2    53 AMDKSAKAPQITIFDHRGCSRAPKESTGGKAGGQDDEMMVKVASTKVTVSESDAAKKLQEFITFEKGIDGPFTSKN 128
               SCOP domains d1xg0a_ A: Phycoerythrin 545 alpha-subunits                                  SCOP domains
               CATH domains 1xg0A00 A:1-76 Cryptophytan Phycoerythrin (Alpha-1 Chain); Chain A           CATH domains
               Pfam domains ------Phycoerythr_ab-1xg0A01 A:7-63                            ------------- Pfam domains
         Sec.struct. author ......eeeeeeeee.................hhhh.eeeeeeeee...hhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 1xg0 A   1 AMDkSAKAPQITIFDHRGCSRAPKESTGGKAGGQDDEMMVKVASTKVTVSESDAAKKLQEFITFEKGIDGPFTSKN  76
                               |    10        20        30        40        50        60        70      
                               4-LYZ                                                                    

Chain B from PDB  Type:PROTEIN  Length:67
 aligned with PHE2_RHDS2 | P30943 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:67
                                    47        57        67        77        87        97       
           PHE2_RHDS2    38 AMDKSAKAPVITIFDHRGCSRAPKEYTGAKAGGKDDEMMVKAQSVKIEVSTGTAEGVLATSLAKMTK 104
               SCOP domains d1xg0b_ B: Phycoerythrin 545 alpha-subunits                         SCOP domains
               CATH domains 1xg0B00 B:1-67 Cryptophytan Phycoerythrin (Alpha-1 Chain); Chain A  CATH domains
               Pfam domains ------Phycoerythr_ab-1xg0B01 B:7-63                            ---- Pfam domains
         Sec.struct. author ......eeeeeeeee.................hhhh.eeeeeeeee...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 1xg0 B   1 AMDKSAKAPVITIFDHRGCSRAPKEYTGAKAGGKDDEMMVKAQSVKIEVSTGTAEGVLATSLAKMTK  67
                                    10        20        30        40        50        60       

Chain C from PDB  Type:PROTEIN  Length:174
 aligned with PHEB_RHDS2 | P27198 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:175
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172     
           PHEB_RHDS2     3 DAFSRVVTNADSKAAYVGGADLQALKKFISEGNKRLDSVNSIVSNASCIVSDAVSGMICENPSLISPSGNCYTNRRMAACLRDGEIILRYVSYALLSGDASVLEDRCLNGLKETYSSLGVPANSNARAVSIMKACAVAFVNNTASQKKLSTPQGDCSGLASEVGGYFDKVTAAIS 177
               SCOP domains d1xg0c_  C: Phycoerythrin beta subunit                                                                                                                                          SCOP domains
               CATH domains 1xg0C00  C:3-177 Phycocyanins                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh-.....eeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xg0 C   3 DAFSRVVT-ADSKAAYVGGADLQALKKFISEGNKRLDSVNSIVSNASCIVSDAVSGMICENPSLISPSGnCYTNRRMAACLRDGEIILRYVSYALLSGDASVLEDRCLNGLKETYSSLGVPANSNARAVSIMKACAVAFVNNTASQKKLSTPQGDCSGLASEVGGYFDKVTAAIS 177
                                   |12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172     
                                  10 |                                                          72-MEN                                                                                                     
                                    12                                                                                                                                                                     

Chain D from PDB  Type:PROTEIN  Length:177
 aligned with PHEB_RHDS2 | P27198 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       
           PHEB_RHDS2     1 MLDAFSRVVTNADSKAAYVGGADLQALKKFISEGNKRLDSVNSIVSNASCIVSDAVSGMICENPSLISPSGNCYTNRRMAACLRDGEIILRYVSYALLSGDASVLEDRCLNGLKETYSSLGVPANSNARAVSIMKACAVAFVNNTASQKKLSTPQGDCSGLASEVGGYFDKVTAAIS 177
               SCOP domains d1xg0d_ D: Phycoerythrin beta subunit                                                                                                                                             SCOP domains
               CATH domains 1xg0D00 D:1-177 Phycocyanins                                                                                                                                                      CATH domains
           Pfam domains (1) -----Phycobilisome-1xg0D01 D:6-177                                                                                                                                                Pfam domains (1)
           Pfam domains (2) -----Phycobilisome-1xg0D02 D:6-177                                                                                                                                                Pfam domains (2)
         Sec.struct. author .hhhhhhhhh......eeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhh......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xg0 D   1 MLDAFSRVVTNADSKAAYVGGADLQALKKFISEGNKRLDSVNSIVSNASCIVSDAVSGMICENPSLISPSGnCYTNRRMAACLRDGEIILRYVSYALLSGDASVLEDRCLNGLKETYSSLGVPANSNARAVSIMKACAVAFVNNTASQKKLSTPQGDCSGLASEVGGYFDKVTAAIS 177
                                    10        20        30        40        50        60        70 |      80        90       100       110       120       130       140       150       160       170       
                                                                                                  72-MEN                                                                                                     

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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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Globin (291)

(-) Gene Ontology  (9, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PHE3_RHDS2 | Q00433)
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009535    chloroplast thylakoid membrane    The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030089    phycobilisome    Any of the granules, approximately 32 nm x 48 nm and consisting of highly aggregated phycobiliproteins, that are attached in arrays to the external face of a thylakoid membrane in algae of the phyla Cyanophyta and Rhodophyta, where they function as light-harvesting devices in photosynthesis. Excitation energy in the phycobilisome flows in the sequence: phycoerythrin, phycocyanin, allophycocyanin before passing to the antenna chlorophyll of photosystem II.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
    GO:0009579    thylakoid    A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.

Chain B   (PHE2_RHDS2 | P30943)
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009535    chloroplast thylakoid membrane    The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030089    phycobilisome    Any of the granules, approximately 32 nm x 48 nm and consisting of highly aggregated phycobiliproteins, that are attached in arrays to the external face of a thylakoid membrane in algae of the phyla Cyanophyta and Rhodophyta, where they function as light-harvesting devices in photosynthesis. Excitation energy in the phycobilisome flows in the sequence: phycoerythrin, phycocyanin, allophycocyanin before passing to the antenna chlorophyll of photosystem II.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
    GO:0009579    thylakoid    A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.

Chain C,D   (PHEB_RHDS2 | P27198)
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009535    chloroplast thylakoid membrane    The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030089    phycobilisome    Any of the granules, approximately 32 nm x 48 nm and consisting of highly aggregated phycobiliproteins, that are attached in arrays to the external face of a thylakoid membrane in algae of the phyla Cyanophyta and Rhodophyta, where they function as light-harvesting devices in photosynthesis. Excitation energy in the phycobilisome flows in the sequence: phycoerythrin, phycocyanin, allophycocyanin before passing to the antenna chlorophyll of photosystem II.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
    GO:0009579    thylakoid    A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.

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  PHE2_RHDS2 | P30943
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  PHE3_RHDS2 | Q00433
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  PHEB_RHDS2 | P27198
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 Related Entries

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

UniProtKB/Swiss-Prot
        PHE2_RHDS2 | P309431qgw 1xf6
        PHE3_RHDS2 | Q004331qgw 1xf6
        PHEB_RHDS2 | P271981qgw 1xf6

(-) Related Entries Specified in the PDB File

1qgw SAME PROTIEN AT 1.63 ANGSTROM
1xf6 SAME PROTEIN AT 1.10 ANGSTROM. (DATA SET 98% COMPLETE)