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(-) Description

Title :  RIBONUCLEOTIDE REDUCTASE E441D MUTANT R1 PROTEIN FROM ESCHERICHIA COLI
 
Authors :  M. Eriksson, H. Eklund
Date :  17 Sep 97  (Deposition) - 18 Mar 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D,E,F,P
Biol. Unit 1:  A,D,P  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,F  (1x)
Biol. Unit 4:  A,B,D,E  (3x)
Biol. Unit 5:  C,F  (6x)
Biol. Unit 6:  A,B  (3x)
Biol. Unit 7:  A,B,D,E  (1x)
Biol. Unit 8:  C,F  (2x)
Biol. Unit 9:  A,D  (1x)
Keywords :  Ribonucleotide Reductase, Deoxyribonucleotide Synthesis, Radical Chemistry, Allosteric Regulation, Specificity, Complex (Oxidoreductase/Peptide) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. L. Persson, M. Eriksson, B. Katterle, S. Potsch, M. Sahlin, B. M. Sjoberg
A New Mechanism-Based Radical Intermediate In A Mutant R1 Protein Affecting The Catalytically Essential Glu441 In Escherichia Coli Ribonucleotide Reductase.
J. Biol. Chem. V. 272 31533 1997
PubMed-ID: 9395490  |  Reference-DOI: 10.1074/JBC.272.50.31533
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
    ChainsA, B, C
    EC Number1.17.4.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneNRDA
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
 
Molecule 2 - RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
    ChainsD, E, F, P
    EngineeredYES
    FragmentC-TERMINAL PORTION, 20 RESIDUES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit ABCDEFP
Biological Unit 1 (1x)A  D  P
Biological Unit 2 (1x) B  E  
Biological Unit 3 (1x)  C  F 
Biological Unit 4 (3x)AB DE  
Biological Unit 5 (6x)  C  F 
Biological Unit 6 (3x)AB     
Biological Unit 7 (1x)AB DE  
Biological Unit 8 (2x)  C  F 
Biological Unit 9 (1x)A  D   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 6R1R)

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1ACAUNKNOWNCYS A:225 , CYS A:462 , CYS A:439 , ASN A:437 , ASP A:441ACTIVE SITE WITH GLUTAMATE 441 MUTATED TO ASPARTATE.
2ACBUNKNOWNCYS B:225 , CYS B:462 , CYS B:439 , ASN B:437 , ASP B:441ACTIVE SITE WITH GLUTAMATE 441 MUTATED TO ASPARTATE.
3ACCUNKNOWNCYS C:225 , CYS C:462 , CYS C:439 , ASN C:437 , ASP C:441ACTIVE SITE WITH GLUTAMATE 441 MUTATED TO ASPARTATE.

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:225 -A:462
2B:225 -B:462
3C:225 -C:462

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 6R1R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 6R1R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 6R1R)

(-) Exons   (0, 0)

(no "Exon" information available for 6R1R)

(-) 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:738
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d6r1ra1 A:1-221 R1 subunit of ribonucleotide reductase, N-terminal domain                                                                                                                                                    d6r1ra2 A:222-738 R1 subunit of ribonucleotide reductase, C-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee...eee...hhhhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.....hhhhhh..hhhhhhhhhh..hhhhhh..hhhhhhhhhh..............hhhhhhhhhhhh........hhhhhhhhhhhhh...eee.hhhhhh..........eeeee....hhhhhhhhhhhhhhhhh..eeeee................hhh.hhhhhhhhhhhh............eeeeee.....hhhh.........hhh.....eeeeee.hhhhhhhh...eeee..hhh...hhhhhhh.hhhhhhhhhhhhh......eeeehhhhhhhhhhhhhhh..eeeeehhhhhh.....hhhh................................eeeee......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh...eeeee.hhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhh........hhhh..hhhhhh........hhhhhhhhhhh..............hhhhh.............eeee......eeee...hhhh......hhh....hhhhhhhhhhhhh........eee.hhh.hhh...hhhhhhhhhhhhh........eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 6r1r A   1 MNQNLLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLDIALPTKPLNDVNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRDGA 738
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730        

Chain B from PDB  Type:PROTEIN  Length:738
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d6r1rb1 B:1-221 R1 subunit of ribonucleotide reductase, N-terminal domain                                                                                                                                                    d6r1rb2 B:222-738 R1 subunit of ribonucleotide reductase, C-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee...eee...hhhhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.....hhhhhh..hhhhhhhhhh..hhhhhh..hhhhhhhhhh..............hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...eee.hhhhhh..........eeeee....hhhhhhhhhhhhhhhhh..eeeee................hhh.hhhhhhhhhhhh............eeeeee.....hhhh.........hhh.....eeeeee.hhhhhhhh...eeee..hhh...hhhhhhh.hhhhhhhhhhhhh......eeeehhhhhhhhhhhhhhh..eeeeehhhhhh.....hhhh................................eeeee......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh...eeeee.hhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhh........hhhh..hhhhhh........hhhhhhhhhhh..............hhhhh.............eeee......eeee...hhhh......hhh....hhhhhhhhhhhhh........eee.hhh.hhh...hhhhhhhhhhhhh........eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 6r1r B   1 MNQNLLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLDIALPTKPLNDVNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRDGA 738
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730        

Chain C from PDB  Type:PROTEIN  Length:738
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d6r1rc1 C:1-221 R1 subunit of ribonucleotide reductase, N-terminal domain                                                                                                                                                    d6r1rc2 C:222-738 R1 subunit of ribonucleotide reductase, C-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee...eee...hhhhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.....hhhhhh..hhhhhhhhhh..hhhhhh..hhhhhhhhhh..............hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...eee.hhhhhh..........eeeee....hhhhhhhhhhhhhhhhh..eeeee................hhh.hhhhhhhhhhhh............eeeeee.....hhhh.........hhh.....eeeeee.hhhhhhhh...eeee..hhh...hhhhhhh.hhhhhhhhhhhhh......eeeehhhhhhhhhhhhhhh..eeeeehhhhhh.....hhhh................................eeeee......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh...eeeee.hhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhh........hhhh..hhhhhh........hhhhhhhhhhh..............hhhhhh............eeee......eeee...hhhh......hhh....hhhhhhhhhhhhh........eee.hhh.hhh...hhhhhhhhhhhhh........eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 6r1r C   1 MNQNLLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLDIALPTKPLNDVNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRDGA 738
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730        

Chain D from PDB  Type:PROTEIN  Length:18
                                                  
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author .........hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 6r1r D 358 VGQIDSEVDTDDLSNFQL 375
                                   367        

Chain E from PDB  Type:PROTEIN  Length:18
                                                  
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author .........hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 6r1r E 358 VGQIDSEVDTDDLSNFQL 375
                                   367        

Chain F from PDB  Type:PROTEIN  Length:18
                                                  
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author .........hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 6r1r F 358 VGQIDSEVDTDDLSNFQL 375
                                   367        

Chain P from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 6r1r P   1 YLVG   4

   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  (2, 6)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 6R1R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 6R1R)

(-) Gene Ontology  (17, 25)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RIR1_ECOLI | P004521qfn 1r1r 1rlr 2r1r 2x0x 2xak 2xap 2xav 2xaw 2xax 2xay 2xaz 2xo4 2xo5 3r1r 3uus 4erm 4erp 4r1r 5cns 5cnt 5cnu 5cnv 5r1r 7r1r
        RIR2_ECOLI | P699241av8 1biq 1jpr 1jqc 1mrr 1mxr 1pfr 1pim 1piu 1piy 1piz 1pj0 1pj1 1pm2 1r1r 1r65 1rib 1rnr 1rsr 1rsv 1xik 1yfd 2alx 2av8 2r1r 2x0x 2xak 2xap 2xav 2xaw 2xax 2xay 2xaz 2xo4 2xo5 2xof 3r1r 3uus 4erm 4erp 4r1r 5ci2 5ci3 5cns 5cnt 5cnu 5cnv 5r1r 7r1r

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 6R1R)