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(-) Description

Title :  PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS (ATRAZINE COMPLEX)
 
Authors :  C. R. D. Lancaster, H. Michel
Date :  01 Aug 97  (Deposition) - 06 Apr 99  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  C,H,L,M
Keywords :  Photosynthetic Reaction Center, Secondary Quinone (Qb), Triazine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. R. Lancaster, H. Michel
Refined Crystal Structures Of Reaction Centres From Rhodopseudomonas Viridis In Complexes With The Herbicide Atrazine And Two Chiral Atrazine Derivatives Also Lead To A New Model Of The Bound Carotenoid.
J. Mol. Biol. V. 286 883 1999
PubMed-ID: 10024457  |  Reference-DOI: 10.1006/JMBI.1998.2532
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOTOSYNTHETIC REACTION CENTER
    Atcc: DSM 133
    Cellular Location: INTRACYTOPLASMIC MEMBRANE (ICM)
    Chains: C
    Collection: DSM 133
    Organism Scientific: BLASTOCHLORIS VIRIDIS
    Organism Taxid: 1079
 
Molecule 2 - PHOTOSYNTHETIC REACTION CENTER
    Cellular Location: INTRACYTOPLASMIC MEMBRANE (ICM)
    Chains: L
    Collection: DSM 133
    Organism Scientific: BLASTOCHLORIS VIRIDIS
    Organism Taxid: 1079
 
Molecule 3 - PHOTOSYNTHETIC REACTION CENTER
    Cellular Location: INTRACYTOPLASMIC MEMBRANE (ICM)
    Chains: M
    Collection: DSM 133
    Organism Scientific: BLASTOCHLORIS VIRIDIS
    Organism Taxid: 1079
 
Molecule 4 - PHOTOSYNTHETIC REACTION CENTER
    Cellular Location: INTRACYTOPLASMIC MEMBRANE (ICM)
    Chains: H
    Collection: DSM 133
    Organism Scientific: BLASTOCHLORIS VIRIDIS
    Organism Taxid: 1079

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : CHLM

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (10, 25)

Asymmetric/Biological Unit (10, 25)
No.NameCountTypeFull Name
1ATZ1Ligand/Ion2-CHLORO-4-ISOPROPYLAMINO-6-ETHYLAMINO -1,3,5-TRIAZINE
2BCB4Ligand/IonBACTERIOCHLOROPHYLL B
3BPB2Ligand/IonBACTERIOPHEOPHYTIN B
4FE21Ligand/IonFE (II) ION
5FME1Mod. Amino AcidN-FORMYLMETHIONINE
6HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
7LDA6Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE
8MQ71Ligand/IonMENAQUINONE-7
9NS51Ligand/Ion15-CIS-1,2-DIHYDRONEUROSPORENE
10SO44Ligand/IonSULFATE ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS L:190 , HIS L:230 , HIS M:217 , GLU M:232 , HIS M:264BINDING SITE FOR RESIDUE FE2 M 500
02AC2SOFTWAREARG H:33 , ARG H:37 , TYR H:41 , HOH H:1059 , HOH H:1060 , HOH H:1061 , ARG M:251BINDING SITE FOR RESIDUE SO4 H 801
03AC3SOFTWAREHOH H:1224 , ASN L:199 , HOH L:1127 , HIS M:143 , ARG M:265BINDING SITE FOR RESIDUE SO4 M 802
04AC4SOFTWARELEU H:246 , ALA M:1 , ARG M:226 , HOH M:1226BINDING SITE FOR RESIDUE SO4 M 803
05AC5SOFTWARETRP M:23 , TYR M:50 , ALA M:53 , SER M:54 , SER M:133 , LDA M:704 , HOH M:1030 , HOH M:1064BINDING SITE FOR RESIDUE SO4 M 804
06AC6SOFTWAREHIS L:168 , MET L:174 , VAL L:177 , SER L:178 , VAL L:182 , MET L:185 , VAL L:220 , BCB L:302 , HOH L:993 , MET M:120 , VAL M:155 , ILE M:177 , TRP M:178 , HIS M:180 , ILE M:181 , LEU M:184 , BPB M:401 , NS5 M:600 , BCB M:806BINDING SITE FOR RESIDUE BCB M 805
07AC7SOFTWAREPRO L:124 , MET L:127 , PHE L:128 , VAL L:157 , PHE L:160 , GLY L:161 , TRP L:167 , HIS L:168 , HIS L:173 , SER L:176 , VAL L:177 , PHE L:241 , GLY L:244 , THR L:248 , BCB L:304 , BPB L:402 , TYR M:195 , TYR M:208 , BCB M:805 , BCB M:806BINDING SITE FOR RESIDUE BCB L 302
08AC8SOFTWAREVAL L:157 , TYR L:162 , PHE L:181 , BCB L:302 , BCB L:304 , PHE M:148 , PHE M:154 , VAL M:155 , LEU M:184 , PHE M:187 , SER M:188 , PHE M:194 , TYR M:195 , HIS M:200 , SER M:203 , ILE M:204 , TYR M:208 , MET M:275 , ALA M:278 , ILE M:282 , BPB M:401 , BCB M:805BINDING SITE FOR RESIDUE BCB M 806
09AC9SOFTWAREPHE L:128 , PHE L:146 , ILE L:150 , HIS L:153 , LEU L:154 , VAL L:157 , BCB L:302 , BPB L:402 , GLY M:201 , ILE M:204 , GLY M:205 , TYR M:208 , GLY M:209 , BCB M:806 , HOH M:991BINDING SITE FOR RESIDUE BCB L 304
10BC1SOFTWAREPHE L:181 , MET L:185 , LEU L:189 , VAL L:220 , PHE M:59 , SER M:63 , ILE M:66 , SER M:123 , LEU M:124 , TRP M:127 , ILE M:144 , ASN M:147 , PHE M:148 , SER M:271 , MET M:275 , BCB M:805 , BCB M:806BINDING SITE FOR RESIDUE BPB M 401
11BC2SOFTWAREPHE L:97 , TRP L:100 , GLU L:104 , VAL L:117 , PHE L:121 , PRO L:124 , TYR L:148 , HIS L:153 , ALA L:237 , BCB L:302 , BCB L:304 , TYR M:208 , LEU M:212 , TRP M:250 , ILE M:254 , MQ7 M:501BINDING SITE FOR RESIDUE BPB L 402
12BC3SOFTWARETYR L:29 , BPB L:402 , ALA M:216 , HIS M:217 , THR M:220 , ALA M:246 , TRP M:250 , ALA M:258 , VAL M:263 , PHE M:270BINDING SITE FOR RESIDUE MQ7 M 501
13BC4SOFTWARETYR C:56 , LYS C:57 , ASN C:58 , VAL C:59 , LYS C:60 , VAL C:61 , LEU C:62 , PHE C:70 , LEU C:71 , MET C:74 , THR C:78 , SER C:82 , CYS C:87 , CYS C:90 , HIS C:91 , LEU C:96 , ALA C:97 , TYR C:104 , ALA C:107 , ARG C:108 , VAL C:212BINDING SITE FOR RESIDUE HEM C 337
14BC5SOFTWARETYR C:89 , TYR C:102 , VAL C:106 , MET C:110 , LEU C:111 , MET C:113 , THR C:114 , CYS C:132 , CYS C:135 , HIS C:136 , PRO C:140 , LEU C:141 , PRO C:142 , LEU C:289 , ARG C:293 , PRO C:301BINDING SITE FOR RESIDUE HEM C 338
15BC6SOFTWAREVAL C:201 , ARG C:202 , VAL C:203 , VAL C:204 , MET C:233 , SER C:237 , LEU C:240 , ASN C:243 , CYS C:244 , CYS C:247 , HIS C:248 , PHE C:253 , GLU C:254 , ARG C:264 , ALA C:267 , TRP C:268 , ARG C:272 , HOH C:938 , HOH C:940 , HOH C:973BINDING SITE FOR RESIDUE HEM C 339
16BC7SOFTWAREHIS C:124 , THR C:128 , GLY C:129 , VAL C:130 , ILE C:236 , GLN C:263 , ILE C:266 , GLY C:270 , ILE C:271 , MET C:273 , VAL C:274 , ASP C:304 , CYS C:305 , CYS C:308 , HIS C:309 , THR C:313 , LYS C:314 , PRO C:315 , HOH C:967 , HOH C:1203 , HOH C:1235BINDING SITE FOR RESIDUE HEM C 340
17BC8SOFTWAREGLY M:117 , THR M:121 , GLY M:159 , CYS M:160 , VAL M:173 , GLY M:176 , HIS M:180 , BCB M:805BINDING SITE FOR RESIDUE NS5 M 600
18BC9SOFTWAREGLU L:212 , ASN L:213 , PHE L:216 , TYR L:222 , SER L:223 , ILE L:224 , GLY L:225 , ALA L:226BINDING SITE FOR RESIDUE ATZ L 502
19CC1SOFTWAREARG H:33 , PRO H:54 , ASP H:56 , LDA L:705 , TRP M:266BINDING SITE FOR RESIDUE LDA H 701
20CC2SOFTWAREASP L:60 , PHE L:62 , TYR M:195 , TRP M:295 , CYS M:296 , ALA M:301BINDING SITE FOR RESIDUE LDA L 702
21CC3SOFTWAREPRO H:42 , VAL H:59 , TYR H:60 , LEU H:62 , TYR H:64 , PRO H:65 , ARG H:80BINDING SITE FOR RESIDUE LDA H 703
22CC4SOFTWARETRP M:23 , ALA M:53 , SER M:54 , ALA M:57 , SER M:126 , SER M:133 , SO4 M:804BINDING SITE FOR RESIDUE LDA M 704
23CC5SOFTWARELDA H:701 , HOH H:1060 , PHE M:256BINDING SITE FOR RESIDUE LDA L 705
24CC6SOFTWAREPHE M:71 , ASN M:72 , TRP M:112BINDING SITE FOR RESIDUE LDA M 706

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5PRC)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Pro C:5 -Pro C:6
2Leu C:152 -Pro C:153
3Gly C:329 -Pro C:330
4Gly M:47 -Pro M:48
5Tyr H:41 -Pro H:42
6Val H:78 -Pro H:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5PRC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5PRC)

(-) Exons   (0, 0)

(no "Exon" information available for 5PRC)

(-) 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 C from PDB  Type:PROTEIN  Length:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d5prcc_ C: Photosynthetic reaction centre (cytochrome subunit)                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 5prcC01 C:1-144,C:315-332 Photosynthetic Reaction Center, subunit C, domain 2                                                                   5prcC02 C:145-314 Photosynthetic Reaction Center, subunit C, domain 2                                                                                                     5prcC01            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee............eeehhhhhhhhhhhhh.............................hhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhh...........hhhhh................................hhhhhhhhhhh.........hhhhh.............................hhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhh..hhhhh.................hhhhh....................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5prc C   1 CFEPPPATTTQTGFRGLSMGEVLHPATVKAKKERDAQYPPALAAVKAEGPPVSQVYKNVKVLGNLTEAEFLRTMTAITEWVSPQEGCTYCHDENNLASEAKYPYVVARRMLEMTRAINTNWTQHVAQTGVTCYTCHRGTPLPPYVRYLEPTLPLNNRETPTHVERVETRSGYVVRLAKYTAYSALNYDPFTMFLANDKRQVRVVPQTALPLVGVSRGKERRPLSDAYATFALMMSISDSLGTNCTFCHNAQTFESWGKKSTPQRAIAWWGIRMVRDLNMNYLAPLNASLPASRLGRQGEAPQADCRTCHQGVTKPLFGASRLKDYPELGPIK 332
                                    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       290       300       310       320       330  


Chain H from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains d5prch2 H:1-36                      d5prch1 H:37-258 Photosynthetic reaction centre                                                                                                                                                                                SCOP domains
               CATH domains -5prcH01 H:2-119 Photosynthetic Reaction Center, subunit H, domain 1                                                   5prcH02 H:120-258 Photosynthetic Reaction Center, subunit H, domain 2                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhh.hhhhhh..................hhhhh.....eeee.....eeee...........eee........eee...hhhh.......................eee...................eee.....eeeeeeeeeee.......eeeeee.....eeeee...eee....eee....hhhhhh...........hhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5prc H   1 mYHGALAQHLDIAQLVWYAQWLVIWTVVLLYLRREDRREGYPLVEPLGLVKLAPEDGQVYELPYPKTFVLPHGGTVTVPRRRPETRELKLAQTDGFEGAPLQPTGNPLVDAVGPASYAERAEVVDATVDGKAKIVPLRVATDFSIAEGDVDPRGLPVVAADGVEAGTVTDLWVDRSEHYFRYLELSVAGSARTALIPLGFCDVKKDKIVVTSILSEQFANVPRLQSRDQITLREEDKVSAYYAGGLLYATPERAESLL 258
                            |       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        
                            1-FME                                                                                                                                                                                                                                                             


Chain L from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains d5prcl_ L: L (light) subunit                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 5prcL01 L:1-160 Membrane spanning alpha-helix pairs                                                                                                             5prcL02 L:161-272 Membrane spanning alpha-helix pairs                                                           - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............................hhhhhhhhhhhhhhhhhhhhhhhh............................hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5prc L   1 ALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWDPFAISINPPDLKYGLGAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLAFCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWHYNPGHMSSVSFLFVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNIFLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS 273
                                    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   


Chain M from PDB  Type:PROTEIN  Length:323
                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d5prcm_ M: M (medium) subunit                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 5prcM01 M:1-143 Membrane spanning alpha-helix pairs                                                                                            5prcM02 M:144-302 Membrane spanning alpha-helix pairs                                                                                                          --------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................................................hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh........................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5prc M   1 ADYQTIYTQIQARGPHITVSGEWGDNDRVGKPFYSYWLGKIGDAQIGPIYLGASGIAAFAFGSTAILIILFNMAAEVHFDPLQFFRQFFWLGLYPPKAQYGMGIPPLHDGGWWLMAGLFMTLSLGSWWIRVYSRARALGLGTHIAWNFAAAIFFVLCIGCIHPTLVGSWSEGVPFGIWPHIDWLTAFSIRYGNFYYCPWHGFSIGFAYGCGLLFAAHGATILAVARFGGDREIEQITDRGTAVERAALFWRWTIGFNATIESVHRWGWFFSLMVMVSASVGILLTGTFVDNWYLWCVKHGAAPDYPAYLPATPDPASLPGAPK 323
                                    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       290       300       310       320
   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  (5, 5)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (4, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Few Secondary Structures (1120)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5PRC)

(-) Gene Ontology  (17, 47)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Pro C:5 - Pro C:6   [ RasMol ]  
    Tyr H:41 - Pro H:42   [ RasMol ]  
    Val H:78 - Pro H:79   [ RasMol ]  
 

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Access by UniProt ID/Accession number
  CYCR_BLAVI | P07173
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  RCEH_BLAVI | P06008
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  RCEL_BLAVI | P06009
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  RCEM_BLAVI | P06010
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CYCR_BLAVI | P07173: 1dxr 1prc 1r2c 1vrn 2i5n 2jbl 2prc 2wjm 2wjn 2x5u 2x5v 3d38 3g7f 3prc 3t6d 3t6e 4ac5 4cas 5m7j 5m7k 5m7l 6prc 7prc
        RCEH_BLAVI | P06008: 1dxr 1prc 1r2c 1vrn 2i5n 2jbl 2prc 2wjm 2wjn 2x5u 2x5v 3d38 3g7f 3prc 3t6d 3t6e 4ac5 4cas 5m7j 5m7k 5m7l 6prc 7prc
        RCEL_BLAVI | P06009: 1dxr 1prc 1r2c 1vrn 2i5n 2jbl 2prc 2wjm 2wjn 2x5u 2x5v 3d38 3g7f 3prc 3t6d 3t6e 4ac5 4cas 5m7j 5m7k 5m7l 6prc 7prc
        RCEM_BLAVI | P06010: 1dxr 1prc 1r2c 1vrn 2i5n 2jbl 2prc 2wjm 2wjn 2x5u 2x5v 3d38 3g7f 3prc 3t6d 3t6e 4ac5 4cas 5m7j 5m7k 5m7l 6prc 7prc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5PRC)