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(-) Description

Title :  DIABODY 305 COMPLEX WITH EPOR
 
Authors :  I. Moraga, F. Guo, E. Ozkan, K. M. Jude, K. C. Garcia
Date :  12 Feb 15  (Deposition) - 18 Mar 15  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.15
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C,J,K,L  (1x)
Biol. Unit 2:  D,E,F,G,H,I  (1x)
Keywords :  Diabody Complex, Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. Moraga, G. Wernig, S. Wilmes, V. Gryshkova, C. P. Richter, W. J. Hong R. Sinha, F. Guo, H. Fabionar, T. S. Wehrman, P. Krutzik, S. Demharter, I. Plo, I. L. Weissman, P. Minary, R. Majeti, S. N. Constantinescu, J. Piehler, K. C. Garcia
Tuning Cytokine Receptor Signaling By Re-Orienting Dimer Geometry With Surrogate Ligands.
Cell V. 160 1196 2015
PubMed-ID: 25728669  |  Reference-DOI: 10.1016/J.CELL.2015.02.011

(-) Compounds

Molecule 1 - DIABODY 310 VL DOMAIN
    ChainsA, D, G, J
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Taxid7111
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - DIABODY 310 VH DOMAIN
    ChainsB, E, H, K
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Taxid7111
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - ERYTHROPOIETIN RECEPTOR
    ChainsC, F, I, L
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Taxid7111
    GeneEPOR
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymEPO-R

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit ABCDEFGHIJKL
Biological Unit 1 (1x)ABC      JKL
Biological Unit 2 (1x)   DEFGHI   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
2PEG17Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 13)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
2PEG12Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1FLC-1Ligand/IonCITRATE ANION
2PEG5Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:26 , PHE A:27 , ASN A:77binding site for residue PEG A 201
02AC2SOFTWAREGLN B:38 , PHE B:63binding site for residue PEG B 201
03AC3SOFTWARELYS A:106 , TRP B:92 , ASP B:94 , ASN B:97binding site for residue PEG B 202
04AC4SOFTWARESER B:27 , ASN B:31 , ASP B:94 , SER L:184binding site for residue PEG B 203
05AC5SOFTWAREASP C:159 , TRP C:212binding site for residue PEG C 301
06AC6SOFTWAREARG C:197binding site for residue PEG C 302
07AC7SOFTWAREARG C:99binding site for residue PEG C 303
08AC8SOFTWAREGLN E:38 , LEU E:40 , PHE E:63binding site for residue PEG E 201
09AC9SOFTWAREARG F:171 , ARG F:197 , ARG I:197binding site for residue PEG F 301
10AD1SOFTWARESER G:54 , ARG G:72 , ASN G:74binding site for residue PEG G 201
11AD2SOFTWAREALA G:40 , LYS G:43 , GLU G:46 , GLN H:1binding site for residue PEG G 202
12AD3SOFTWAREGLN H:38 , PHE H:63 , ASP H:83binding site for residue PEG H 201
13AD4SOFTWAREGLY J:9binding site for residue PEG J 201
14AD5SOFTWARETRP K:92 , ASP K:94 , ASN K:97 , PHE L:93binding site for residue PEG K 201
15AD6SOFTWAREGLN K:38 , GLY K:58 , SER K:60 , PHE K:63 , GLU K:82 , ASP K:83binding site for residue FLC K 202
16AD7SOFTWAREASP L:159binding site for residue PEG L 301
17AD8SOFTWAREHIS L:70binding site for residue PEG L 302
18AD9SOFTWAREGLN L:58binding site for residue PEG L 303

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:22 -A:96
2B:22 -B:89
3C:28 -C:38
4C:67 -C:83
5D:22 -D:96
6E:22 -E:89
7F:28 -F:38
8F:67 -F:83
9G:22 -G:96
10H:22 -H:89
11I:28 -I:38
12I:67 -I:83
13J:22 -J:96
14K:22 -K:89
15L:28 -L:38
16L:67 -L:83

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ala C:132 -Asp C:133
2Glu C:202 -Pro C:203
3Glu F:202 -Pro F:203
4Arg I:76 -Gly I:77
5Glu I:202 -Pro I:203
6Glu L:202 -Pro L:203

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y5X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y5X)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y5X)

(-) 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:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee.....hhhhh.eee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y5x A   1 EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCVKDRVAVAGKGSYYFDSWGRGTTVTVSS 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    

Chain B from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee....eeeeeee..........eeeeee......eeee.............eeeee...eeeeeee..hhhhh.eeeeeee......eee...eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 4y5x B   1 QSVLTQPPSVSEAPGQRVTIACSGSSSNIGNNAVSWYQQLPGKAPTLLIYYDNLLPSGVSDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNDWVFGGGTKVTVLA 111
                                    10        20        30        40        50        60        70        80        90       100       110 

Chain C from PDB  Type:PROTEIN  Length:205
                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.......eee.......eeeeee....eeeeeee.....eee.eeeeee...eeeeeee.hhhhh.....eeeeeee....eeeeeeehhhhh......eeeeee......eeeeee......hhh.eeeeeeee......eeeeeee.....eeee.......eeeeeeeeee...............eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y5x C  11 FESKAALLAARGPEELLCFTERLEDLVCFWEEAPGQYSFSYQLEDEPWKLCRLHQAPTARGAVRFWCSLPTADTSSFVPLELRVTAASGAPRYHRVIHINEVVLLDAPVGLVARLADESHVVLRWLPPPETPMTSHIRYEVDVSAGQGAGSVQRVEILEGRTECVLSNLRGRTRYTFAVRARMAEPSFGGFWSAWSEPVSLLTPS 222
                                    20        30        40  ||    56        66        76        86        96       106       116       126       137       147       157       167       177       187       197       207       217     
                                                           43|                                                                                  135|                                                                                     
                                                            50                                                                                   137                                                                                     

Chain D from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee.....hhhhh.eee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y5x D   1 EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCVKDRVAVAGKGSYYFDSWGRGTTVTVSS 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    

Chain E from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee..........eeeeee......eeee.............eeeee...eeeeee...hhhhh.eeeeeee......eee...eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 4y5x E   1 QSVLTQPPSVSEAPGQRVTIACSGSSSNIGNNAVSWYQQLPGKAPTLLIYYDNLLPSGVSDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNDWVFGGGTKVTVLA 111
                                    10        20        30        40        50        60        70        80        90       100       110 

Chain F from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh....eee......eeeeeee....eeeeeee.....eee.eeeeee...eeeeeeeehhhhh.....eeeeeee....eeeeeeehhhhh......eeeeeee......eeeeee......hhh.eeeeeeee......eeeeeee.....eeee.......eeeeeeeeee...............eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y5x F  11 FESKAALLAARGPEELLCFTERLEDLVCFWEEAAGQYSFSYQLEDEPWKLCRLHQAPTARGAVRFWCSLPTADTSSFVPLELRVTAASGAPRYHRVIHINEVVLLDAPVGLVARLADESGHVVLRWLPPPETPMTSHIRYEVDVSAGQGAGSVQRVEILEGRTECVLSNLRGRTRYTFAVRARMAEPSFGGFWSAWSEPVSLLTPS 222
                                    20        30        40   ||   56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216      
                                                            44|                                                                                                                                                                           
                                                             51                                                                                                                                                                           

Chain G from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee....eeeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeeee..hhhhheeeeeeee.....hhhhh.eee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y5x G   1 EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCVKDRVAVAGKGSYYFDSWGRGTTVTVSS 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    

Chain H from PDB  Type:PROTEIN  Length:109
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee.....eeeeeee..........eeeeee......eeee.............eeeee...eeeeeee..hhhhh.eeeeeeee....eeee...eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 4y5x H   1 QSVLTQPPSVSEAPGQRVTIACSGSSSNIGNNAVSWYQQLPGKAPTLLIYYDNLLPSGVSDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNDWVFGGGTKVTV 109
                                    10        20        30        40        50        60        70        80        90       100         

Chain I from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.......eee.......eeeeee....eeeeeee.....eee.eeeeee...eeeeeee.hhhhh.....eeeeeee....eeeeeeehhhhh......eeeee..........eeee......hhh.eeeeeeeee....eeeeeeee.....ee.........eeeeeeeeee...............eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y5x I  10 KFESKAALLAARGPEELLCFTERLEDLVCFWEEAPGQYSFSYQLEDEPWKLCRLHQAPTARGAVRFWCSLPTADTSSFVPLELRVTAASGAPRYHRVIHINEVVLLDAPVGLVARLADESGHVVLRWLPPPETPMTSHIRYEVDVSAGQGAGSVQRVEILEGRTECVLSNLRGRTRYTFAVRARMAEPSFGGFWSAWSEPVSLLTPS 222
                                    19        29        39   ||   55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       
                                                            43|                                                                                                                                                                            
                                                             50                                                                                                                                                                            

Chain J from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee....eeeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.......eeeeee....eeeeeee..hhhhheeeeeeee.....hhhhh.eee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y5x J   1 EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCVKDRVAVAGKGSYYFDSWGRGTTVTVSS 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    

Chain K from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee...........eeeee......eeee.............eeeee...eeeeee...hhhhh.eeeeeee......eee...eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 4y5x K   1 QSVLTQPPSVSEAPGQRVTIACSGSSSNIGNNAVSWYQQLPGKAPTLLIYYDNLLPSGVSDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNDWVFGGGTKVTVLA 111
                                    10        20        30        40        50        60        70        80        90       100       110 

Chain L from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.....eee.......eeeeee....eeeeeee.....eee.eeeee...eeeeee.hhhhh.....eeeeeee....eeeeeeehhhhh......eeeeeee......eeeeee......hhh.eeeeeeeee....eeeeeeee.....eeee.......eeeeeeeeee...............eeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y5x L  11 FESKAALLAARGPEELLCFTERLEDLVCFWEEAPGQYSFSYQLEDEPWKLCRLHQAPTAAVRFWCSLPTADTSSFVPLELRVTAASGAPRYHRVIHINEVVLLDAPVGLVARLADESGHVVLRWLPPPETPMTSHIRYEVDVSAGQGAGSVQRVEILEGRTECVLSNLRGRTRYTFAVRARMAEPSFGGFWSAWSEPVSLLTPSDL 224
                                    20        30        40  ||    56        66        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218      
                                                           43|                       75|                                                                                                                                                  
                                                            50                        78                                                                                                                                                  

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 4Y5X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y5X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y5X)

(-) Gene Ontology  (32, 33)

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 Related Entries

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

UniProtKB/Swiss-Prot
        EPOR_HUMAN | P192351cn4 1eba 1ebp 1eer 1ern 2jix 2mv6 4y5v 4y5y

(-) Related Entries Specified in the PDB File

4y5v 4y5y