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(-) Description

Title :  2.70 A CYTOCHROME B6F COMPLEX STRUCTURE FROM NOSTOC PCC 7120
 
Authors :  S. S. Hasan, E. Yamashita, D. Baniulis, W. A. Cramer
Date :  16 Sep 12  (Deposition) - 20 Feb 13  (Release) - 03 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D,E,F,G,H  (2x)
Keywords :  Alpha Helix, Beta-Sheet, Plastoquinol-Plastocyanin Oxidoreductase, Plastocyanin, Thylakoid Membranes, Photosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. S. Hasan, E. Yamashita, D. Baniulis, W. A. Cramer
Quinone-Dependent Proton Transfer Pathways In The Photosynthetic Cytochrome B6F Complex
Proc. Natl. Acad. Sci. Usa V. 110 4297 2013
PubMed-ID: 23440205  |  Reference-DOI: 10.1073/PNAS.1222248110

(-) Compounds

Molecule 1 - CYTOCHROME B6
    ChainsA
    Organism ScientificNOSTOC
    Organism Taxid103690
    StrainPCC 7120
 
Molecule 2 - CYTOCHROME B6-F COMPLEX SUBUNIT 4
    ChainsB
    Organism ScientificNOSTOC
    Organism Taxid103690
    StrainPCC 7120
    Synonym17 KDA POLYPEPTIDE
 
Molecule 3 - APOCYTOCHROME F
    ChainsC
    Organism ScientificNOSTOC
    Organism Taxid103690
    StrainPCC 7120
 
Molecule 4 - CYTOCHROME B6-F COMPLEX IRON-SULFUR SUBUNIT 1
    ChainsD
    EC Number1.10.9.1
    Organism ScientificNOSTOC
    Organism Taxid103690
    StrainPCC 7120
 
Molecule 5 - CYTOCHROME B6-F COMPLEX SUBUNIT 6
    ChainsE
    Organism ScientificNOSTOC
    Organism Taxid103690
    StrainPCC 7120
    SynonymCYTOCHROME B6-F COMPLEX SUBUNIT PETL, CYTOCHROME B6-F COMPLEX SUBUNIT VI
 
Molecule 6 - CYTOCHROME B6-F COMPLEX SUBUNIT 7
    ChainsF
    Organism ScientificNOSTOC
    Organism Taxid103690
    StrainPCC 7120
    SynonymCYTOCHROME B6-F COMPLEX SUBUNIT PETM, CYTOCHROME B6-F COMPLEX SUBUNIT VII
 
Molecule 7 - CYTOCHROME B6-F COMPLEX SUBUNIT 5
    ChainsG
    Organism ScientificNOSTOC
    Organism Taxid103690
    StrainPCC 7120
    SynonymCYTOCHROME B6-F COMPLEX SUBUNIT PETG, CYTOCHROME B6-F COMPLEX SUBUNIT V
 
Molecule 8 - CYTOCHROME B6-F COMPLEX SUBUNIT 8
    ChainsH
    Organism ScientificNOSTOC
    Organism Taxid103690
    StrainPCC 7120
    SynonymCYTOCHROME B6-F COMPLEX SUBUNIT PETN, CYTOCHROME B6-F COMPLEX SUBUNIT VIII

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (2x)ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (12, 20)

Asymmetric Unit (12, 20)
No.NameCountTypeFull Name
17PH1Ligand/Ion(1R)-2-(DODECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYLTETRADECANOATE
28K61Ligand/IonOCTADECANE
3BCR1Ligand/IonBETA-CAROTENE
4CD1Ligand/IonCADMIUM ION
5CLA1Ligand/IonCHLOROPHYLL A
6FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
7HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
8MYS1Ligand/IonPENTADECANE
9OCT1Ligand/IonN-OCTANE
10OPC2Ligand/Ion(7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE
11SQD1Ligand/Ion1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
12UMQ5Ligand/IonUNDECYL-MALTOSIDE
Biological Unit 1 (11, 38)
No.NameCountTypeFull Name
17PH2Ligand/Ion(1R)-2-(DODECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYLTETRADECANOATE
28K62Ligand/IonOCTADECANE
3BCR2Ligand/IonBETA-CAROTENE
4CD-1Ligand/IonCADMIUM ION
5CLA2Ligand/IonCHLOROPHYLL A
6FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
7HEM8Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
8MYS2Ligand/IonPENTADECANE
9OCT2Ligand/IonN-OCTANE
10OPC4Ligand/Ion(7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE
11SQD2Ligand/Ion1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
12UMQ10Ligand/IonUNDECYL-MALTOSIDE

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:47 , PHE A:48 , GLY A:51 , PHE A:52 , MET A:54 , ARG A:83 , HIS A:86 , ARG A:87 , ALA A:90 , THR A:128 , PHE A:131 , GLY A:135 , LEU A:138 , PRO A:139 , HIS A:187 , PHE A:189 , HOH A:422BINDING SITE FOR RESIDUE HEM A 301
02AC2SOFTWARETYR A:34 , GLY A:37 , GLY A:38 , THR A:40 , MET A:93 , HIS A:100 , VAL A:101 , ARG A:103 , VAL A:104 , GLY A:109 , ARG A:114 , THR A:117 , TRP A:118 , GLY A:121 , VAL A:122 , MET A:199 , HIS A:202 , PHE A:203 , ILE A:206 , ILE A:211 , SER A:212 , HEM A:303 , HOH A:401 , HOH A:409 , HOH A:413BINDING SITE FOR RESIDUE HEM A 302
03AC3SOFTWARETYR A:34 , CYS A:35 , GLY A:38 , LEU A:41 , ILE A:206 , ARG A:207 , GLY A:210 , ILE A:211 , HEM A:302 , UMQ A:307 , HOH A:401 , HOH A:416 , HOH A:425 , HOH A:426 , VAL B:39 , PHE B:40 , ARG H:26BINDING SITE FOR RESIDUE HEM A 303
04AC4SOFTWAREASN A:3 , TYR A:5 , ILE A:17 , ALA A:18 , UMQ A:305 , SQD D:201BINDING SITE FOR RESIDUE UMQ A 304
05AC5SOFTWAREALA A:18 , GLU A:19 , THR A:22 , UMQ A:304 , UMQ A:307 , TRP B:32 , ASN C:288 , SQD D:201BINDING SITE FOR RESIDUE UMQ A 305
06AC6SOFTWARESER A:130 , CLA B:201BINDING SITE FOR RESIDUE MYS A 306
07AC7SOFTWARELYS A:24 , ARG A:207 , HEM A:303 , UMQ A:305 , HOH A:407 , ALA B:31 , LEU B:36 , PHE B:40BINDING SITE FOR RESIDUE UMQ A 307
08AC8SOFTWAREMET A:1 , ALA A:2 , VAL A:4 , TRP A:7BINDING SITE FOR RESIDUE UMQ A 309
09AC9SOFTWAREILE A:98 , PHE A:102 , TYR A:105 , ALA A:125 , VAL A:129 , MYS A:306 , TYR B:80 , PRO B:83 , VAL B:84 , LEU B:108 , VAL B:132 , PHE B:133 , GLY B:136 , VAL B:139 , THR B:140 , OPC B:202 , HOH B:301 , HOH B:306 , HOH B:318 , UMQ F:101BINDING SITE FOR RESIDUE CLA B 201
10BC1SOFTWARETYR A:105 , ILE B:87 , SER B:103 , VAL B:104 , GLY B:107 , ILE B:114 , GLU B:115 , ASN B:118 , ARG B:126 , VAL B:128 , ALA B:129 , CLA B:201 , HOH B:304BINDING SITE FOR RESIDUE OPC B 202
11BC2SOFTWARETYR C:1 , PRO C:2 , TRP C:4 , ALA C:5 , CYS C:22 , CYS C:25 , HIS C:26 , GLN C:60 , LEU C:70 , ASN C:71 , VAL C:72 , GLY C:73 , ALA C:74 , ASN C:154 , GLY C:156 , ARG C:157 , GLY C:158 , VAL C:160 , TYR C:161 , HOH C:440BINDING SITE FOR RESIDUE HEM C 301
12BC3SOFTWAREPRO C:37 , GLN C:38 , SER C:39 , ALA E:3 , TYR E:7 , GLU F:4 , LEU F:11 , BCR G:101 , MET H:1 , LEU H:12 , PHE H:15BINDING SITE FOR RESIDUE OPC C 302
13BC4SOFTWAREPHE A:78 , VAL B:52 , ASP C:251 , TRP C:257 , GLY D:33 , ALA D:34 , TYR D:36BINDING SITE FOR RESIDUE 7PH C 303
14BC5SOFTWAREASN A:74 , HIS C:143BINDING SITE FOR RESIDUE CD C 304
15BC6SOFTWAREUMQ A:304 , UMQ A:305 , TRP B:32 , TYR B:38 , HOH B:305 , LYS C:275 , ARG D:16 , ASN D:20BINDING SITE FOR RESIDUE SQD D 201
16BC7SOFTWARECYS D:108 , HIS D:110 , LEU D:111 , CYS D:126 , HIS D:129 , SER D:131BINDING SITE FOR RESIDUE FES D 202
17BC8SOFTWARETHR B:140 , LEU B:141 , ILE B:145 , LEU B:149 , CLA B:201 , MET F:1 , SER F:2 , LEU F:5 , VAL G:2 , SER G:7BINDING SITE FOR RESIDUE UMQ F 101
18BC9SOFTWARETRP F:20 , ALA F:24BINDING SITE FOR RESIDUE OCT F 102
19CC1SOFTWAREPHE A:33 , ILE A:39 , MET A:96 , OPC C:302 , ILE F:16 , VAL G:16 , ALA G:19 , GLY G:20 , TYR G:23 , SER H:18 , ILE H:19BINDING SITE FOR RESIDUE BCR G 101

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1D:108 -D:126
2D:113 -D:128

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:112 -Pro A:113
2Trp B:32 -Pro B:33

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H44)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H44)

(-) Exons   (0, 0)

(no "Exon" information available for 4H44)

(-) 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:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh..ee....hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h44 A   1 MANVYDWFEERLEIQAIAEDVTSKYVPPHVNIFYCLGGITLVCFLIQFATGFAMTFYYKPTVAEAYSSVQYIMNEVNFGWLIRSIHRWSASMMVLMMILHVFRVYLTGGFKKPRELTWVSGVILAVITVSFGVTGYSLPWDQVGYWAVKIVSGVPEAIPVVGVLISDLLRGGSSVGQATLTRYYSAHTFVLPWLIAVFMLFHFLMIRKQGISGPL 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     

Chain B from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhh........ee........hhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h44 B   1 MATHKKPDLSDPTLRAKLAKGMGHNYYGEPAWPNDLLYVFPIVIMGSFACIVALAVLDPAMTGEPANPFATPLEILPEWYLYPVFQILRSLPNKLLGVLAMASVPLGLILVPFIENVNKFQNPFRRPVATTVFLFGTLVTLWLGIGAALPLDKSLTLGLF 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain C from PDB  Type:PROTEIN  Length:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh..........hhhhhh.......eee...ee....eeeeeee........ee.....ee..eeeeeee.....ee.hhhhhhhhhhhhhh...eee.......eeeeeeee.....eeeeeee..hhhhh.....eeeeeeeeeee......................ee..............eeee...........eeee...........ee.............eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h44 C   1 YPFWAQQTYPETPREPTGRIVCANCHLAAKPTEVEVPQSVLPDTVFKAVVKIPYDTSVQQVGADGSKVGLNVGAVLMLPEGFKIAPEDRIPEELKEEIGDVYFQPYGEDKDNIVIVGPLPGEQYQEIVFPVLSPNPANDKNIHFGKYSVHVGGNRGRGQVYPTGEKSNNNLYSAAATGTISKIAKQEGEDGSVKYLVDIKTESGEVVSDTIPAGPELIVSEGQAVTAGDALTNNPNVGGFGQLDAEIVLQDANRVGWLIAFVALVMLAQVMLVLKKKQVEKVQAAEMNF 289
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280         

Chain D from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhh.....eeee.hhh.eeee.....eeee...........ee....ee.........................eeeee......eeee............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h44 D   9 DVPDMGRRQFMNLLTFGTVTGVALGALYPVVNYFIPPAAGGAGGGTTAKDELGNDVSVSKFLESHNVGDRTLVQGLKGDPTYIVAITDYGINAVCTHLGCVVPWNAAENKFKCPCHGSQYDATGKVVRGPAPKSLALSHAKTENDKIVLTSWTETDFRTGEEPWWS 179
                                    18        28        38        48        58        68        78        88   ||  103       113       123       133       143       153       163       173      
                                                                                                              92|                                                                                 
                                                                                                               98                                                                                 

Chain E from PDB  Type:PROTEIN  Length:31
                                                               
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                 4h44 E   1 MLAIVAYIGFLALFTGIAAGLLFGLRSAKIL  31
                                    10        20        30 

Chain F from PDB  Type:PROTEIN  Length:32
                                                                
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------- PROSITE
                 Transcript -------------------------------- Transcript
                 4h44 F   1 MSGELLNAALLSFGLIFVGWALGALLLKIQGA  32
                                    10        20        30  

Chain G from PDB  Type:PROTEIN  Length:37
                                                                     
               SCOP domains ------------------------------------- SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                 4h44 G   1 MVEPLLSGIVLGLIVVTLAGLFYAAYKQYKRPNELGG  37
                                    10        20        30       

Chain H from PDB  Type:PROTEIN  Length:29
                                                             
               SCOP domains ----------------------------- SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE ----------------------------- PROSITE
                 Transcript ----------------------------- Transcript
                 4h44 H   1 MAILTLGWVSLLVVFTWSIAMVVWGRNGL  29
                                    10        20         

   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (0, 0)

(no "SCOP Domain" information available for 4H44)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H44)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H44)

(-) Gene Ontology  (23, 85)

Asymmetric Unit(hide GO term definitions)

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  CYB6_NOSS1 | P0A384
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CYF_NOSS1 | Q93SW9
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  PETD_NOSS1 | Q93SX1
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  PETG_NOSS1 | P58246
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  PETL_NOSS1 | Q8YVQ2
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  PETN_NOSS1 | P61048
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 Related Entries

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

UniProtKB/Swiss-Prot
        CYB6_NOSS1 | P0A3842zt9 4ogq
        CYF_NOSS1 | Q93SW91tu2 2zt9 4ogq
        PETD_NOSS1 | Q93SX12zt9 4ogq
        PETG_NOSS1 | P582462zt9 4ogq
        PETL_NOSS1 | Q8YVQ22zt9 4ogq
        PETM_NOSS1 | P0A3Y12zt9 4ogq
        PETN_NOSS1 | P610482zt9 4ogq
        UCRIA_NOSS1 | Q93SX02zt9 4ogq

(-) Related Entries Specified in the PDB File

1q90 1vf5 2d2c 2e74 2e75 2e76 2zt9 4h0l 4h13