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(-) Description

Title :  CONTEXT-INDEPENDENT ANTI-HYPUSINE ANTIBODY FABHPU24.B IN COMPLEX WITH HYPUSINE
 
Authors :  Q. Zhai, P. J. Carter
Date :  17 Sep 15  (Deposition) - 20 Jan 16  (Release) - 04 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F,H,L,M,N,P,Q
Biol. Unit 1:  A,B,Q  (1x)
Biol. Unit 2:  C,D,P  (1x)
Biol. Unit 3:  E,F,M  (1x)
Biol. Unit 4:  H,L,N  (1x)
Keywords :  Hypusine, Antibody, Fabhpu24. B, Eif5A, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Zhai, M. He, A. Song, K. Deshayes, V. M. Dixit, P. J. Carter
Structural Analysis And Optimization Of Context-Independent Anti-Hypusine Antibodies.
J. Mol. Biol. V. 428 603 2016
PubMed-ID: 26778617  |  Reference-DOI: 10.1016/J.JMB.2016.01.006

(-) Compounds

Molecule 1 - FAB HPU24.B HEAVY CHAIN
    Chains: A, C, E, H
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
 
Molecule 2 - FAB HOU24.B LIGHT CHAIN
    Chains: B, D, F, L
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
 
Molecule 3
    Chains: P, Q, M, N
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFHLMNPQ
Biological Unit 1 (1x): AB         Q
Biological Unit 2 (1x):   CD      P 
Biological Unit 3 (1x):     EF  M   
Biological Unit 4 (1x):       HL N  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
15CT4Mod. Amino AcidHYPUSINE
2PCA2Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
15CT1Mod. Amino AcidHYPUSINE
2PCA-1Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
15CT1Mod. Amino AcidHYPUSINE
2PCA-1Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
15CT1Mod. Amino AcidHYPUSINE
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
15CT1Mod. Amino AcidHYPUSINE
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 5DSC)

(-) SS Bonds  (23, 23)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:127 -B:211
3A:140 -A:193
4B:23 -B:88
5B:80 -B:170
6B:134 -B:193
7C:22 -C:92
8C:127 -D:211
9C:140 -C:193
10D:23 -D:88
11D:80 -D:170
12D:134 -D:193
13E:22 -E:92
14E:127 -F:211
15E:140 -E:193
16F:23 -F:88
17F:80 -F:170
18F:134 -F:193
19H:22 -H:92
20H:140 -H:193
21L:23 -L:88
22L:80 -L:170
23L:134 -L:193

(-) Cis Peptide Bonds  (16, 16)

Asymmetric Unit
No.Residues
1Leu A:146 -Pro A:147
2Glu A:148 -Pro A:149
3Ser B:9 -Pro B:10
4Phe B:140 -Pro B:141
5Leu C:146 -Pro C:147
6Glu C:148 -Pro C:149
7Ser D:9 -Pro D:10
8Phe D:140 -Pro D:141
9Leu E:146 -Pro E:147
10Glu E:148 -Pro E:149
11Ser F:9 -Pro F:10
12Phe F:140 -Pro F:141
13Leu H:146 -Pro H:147
14Glu H:148 -Pro H:149
15Ser L:9 -Pro L:10
16Phe L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DSC)

(-) 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:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee..hhh.eeeeeeee......eeeeeee.....eee.......eeeee...eeeeee...hhhhheeeeeeeeeee..eeeeeeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dsc A    2 EQLKESGGRLVAPGTPLTLTCTVSGFDISDYAMIWVRQAPGKGLEWIGIIYGVINDLAYAKWAKGRFTISRTSTTVDLKITSPTTEDTATYFCARGYGSMDGYDRLNLWGQGTLVTVSSGQPKGPSVFPLAPCPSSTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLSSVVSVTSSSQPVTCNVAHPATNTKVDKTVAP  210
                                    11        21        31        41        51 |      60        70        80  |     89        99 ||||| 104       114       124  ||   138       148       158       168       178       188       198       208  
                                                                             52A                            82A               100A||||                        127|                                                                              
                                                                                                                               100B|||                         132                                                                              
                                                                                                                                100C||                                                                                                          
                                                                                                                                 100D|                                                                                                          
                                                                                                                                  100E                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....eeee...eeeeeee....hhhhh.eeeeee......eeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeee...hhhhhee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dsc B    4 LTQTPSPVSAAVGGTVTISCRSRQRVYLGDWLSWFQKKPGQPPKLLIYDASFRGDGVSSRFSGSGSGTHFTLTISGVQCDDAATYYCLGGYYDDADDTFGGGTEVVVKGDPVAPTVLIFPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSSTLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDC  211
                                    13        23    ||  31        41        51        61        71        81        91    ||  99       109       119       129       139       149       159       169       179       189       199       209  
                                                  27A|                                                                  95A|                                                                                                                    
                                                   27B                                                                   95B                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee..hhh.eeeeeeee.....eeeeeeee.....eee.......eeeee...eeeeee...hhhhheeeeeeeeeee..eeeeeeee...eeeee........eeeee......eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee......eeeeeeehhhheeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5dsc C    2 EQLKESGGRLVAPGTPLTLTCTVSGFDISDYAMIWVRQAPGKGLEWIGIIYGVINDLAYAKWAKGRFTISRTSTTVDLKITSPTTEDTATYFCARGYGSMDGYDRLNLWGQGTLVTVSSGQPKGPSVFPLAPCSSTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLSSVVSVTSSSQPVTCNVAHPATNTKVDKTVA  209
                                    11        21        31        41        51 |      60        70        80  |     89        99 ||||| 104       114       124  ||   139       149       159       169       179       189       199       209
                                                                             52A                            82A               100A||||                        127|                                                                            
                                                                                                                               100B|||                         133                                                                            
                                                                                                                                100C||                                                                                                        
                                                                                                                                 100D|                                                                                                        
                                                                                                                                  100E                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....eeee...eeeeeee....hhhhh.eeeeee......eeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeee...hhhhhee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dsc D    4 LTQTPSPVSAAVGGTVTISCRSRQRVYLGDWLSWFQKKPGQPPKLLIYDASFRGDGVSSRFSGSGSGTHFTLTISGVQCDDAATYYCLGGYYDDADDTFGGGTEVVVKGDPVAPTVLIFPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSSTLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDC  211
                                    13        23    ||  31        41        51        61        71        81        91    ||  99       109       119       129       139       149       159       169       179       189       199       209  
                                                  27A|                                                                  95A|                                                                                                                    
                                                   27B                                                                   95B                                                                                                                    


Chain E from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhh.eeeeeeee.....eeeeeeee.....eee.......eeeee...eeeeee...hhhhheeeeeeeeeee..eeeeeeee...eeeee........eeeee........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee..eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dsc E    1 xEQLKESGGRLVAPGTPLTLTCTVSGFDISDYAMIWVRQAPGKGLEWIGIIYGVINDLAYAKWAKGRFTISRTSTTVDLKITSPTTEDTATYFCARGYGSMDGYDRLNLWGQGTLVTVSSGQPKGPSVFPLAPCCGPSSTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLSSVVSVTSPVTCNVAHPATNTKVDKTVAPS  211
                            |       10        20        30        40        50  |     59        69        79   |    88        98  |||||103       113       123     ||135       145       155       165       175       185||     198       208   
                            1-PCA                                             52A                            82A               100A||||                          129|                                                   186|                     
                                                                                                                                100B|||                           132                                                    190                     
                                                                                                                                 100C||                                                                                                          
                                                                                                                                  100D|                                                                                                          
                                                                                                                                   100E                                                                                                          


Chain F from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee....eeeeee....hhhhh.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...hhhhhee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dsc F    5 TQTPSPVSAAVGGTVTISCRSRQRVYLGDWLSWFQKKPGQPPKLLIYDASFRGDGVSSRFSGSGSGTHFTLTISGVQCDDAATYYCLGGYYDDADDTFGGGTEVVVKGDPVAPTVLIFPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSSTLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDC  211
                                    14        24   ||   32        42        52        62        72        82        92   ||  100       110       120       130       140       150       160       170       180       190       200       210 
                                                 27A|                                                                  95A|                                                                                                                    
                                                  27B                                                                   95B                                                                                                                    


Chain H from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhh.eeeeeeee.....eeeeeeee.....eee.......eeeee...eeeeee...hhhhheeeeeeeeeee..eeeeeeee...eeeee........eeeee.....eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee......eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dsc H    1 xEQLKESGGRLVAPGTPLTLTCTVSGFDISDYAMIWVRQAPGKGLEWIGIIYGVINDLAYAKWAKGRFTISRTSTTVDLKITSPTTEDTATYFCARGYGSMDGYDRLNLWGQGTLVTVSSGQPKGPSVFPLAPSSTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLSSVVSVTSSSQPVTCNVAHPATNTKVDKTVAP  210
                            |       10        20        30        40        50  |     59        69        79   |    88        98  |||||103       113       123  ||   139       149       159       169       179       189       199       209 
                            1-PCA                                             52A                            82A               100A||||                       126|                                                                             
                                                                                                                                100B|||                        133                                                                             
                                                                                                                                 100C||                                                                                                        
                                                                                                                                  100D|                                                                                                        
                                                                                                                                   100E                                                                                                        


Chain L from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....eeee....eeeeee....hhhhh.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...hhhhhee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh...eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dsc L    4 LTQTPSPVSAAVGGTVTISCRSRQRVYLGDWLSWFQKKPGQPPKLLIYDASFRGDGVSSRFSGSGSGTHFTLTISGVQCDDAATYYCLGGYYDDADDTFGGGTEVVVKGDPVAPTVLIFPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSSTLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNR  208
                                    13        23    ||  31        41        51        61        71        81        91    ||  99       109       119       129       139       149       159       169       179       189       199         
                                                  27A|                                                                  95A|                                                                                                                 
                                                   27B                                                                   95B                                                                                                                 


Chain M from PDB  Type:PROTEIN  Length:5
                                      
               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
                5dsc M    3 GxGSG    7
                             |   
                             4-5CT


Chain N from PDB  Type:PROTEIN  Length:5
                                      
               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
                5dsc N    3 GxGSG    7
                             |   
                             |   
                             4-5CT


Chain P from PDB  Type:PROTEIN  Length:5
                                      
               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
                5dsc P    3 GxGSG    7
                             |   
                             |   
                             4-5CT


Chain Q from PDB  Type:PROTEIN  Length:5
                                      
               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
                5dsc Q    3 GxGSG    7
                             |   
                             |   
                             4-5CT
   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

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 Related Entries

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(-) Related Entries Specified in the PDB File

5drn 5ds8 5dtf 5dub