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(-) Description

Title :  PVHL:ELOB:ELOC IN COMPLEX WITH (2S,4R)-1-(3,3-DIMETHYLBUTANOYL)-4-HYDROXY-N-(4-(OXAZOL-5-YL)BENZYL)PYRROLIDINE-2-CARBOXAMIDE (LIGAND 2)
 
Authors :  M. S. Gadd, S. Hewitt, C. Galdeano, I. Van Molle, A. Ciulli
Date :  27 Aug 14  (Deposition) - 10 Sep 14  (Release) - 05 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Biol. Unit 3:  G,H,I  (1x)
Biol. Unit 4:  J,K,L  (1x)
Keywords :  Protein Complex, Ubiquitin Ligase, Hypoxia Inducible Factor, Transcription, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Galdeano, M. S. Gadd, P. Soares, S. Scaffidi, I. Van Molle, I. Birced, S. Hewitt, D. M. Dias, A. Ciulli
Structure-Guided Design And Optimization Of Small Molecules Targeting The Protein-Protein Interaction Between The Von Hippel-Lindau (Vhl) E3 Ubiquitin Ligase And The Hypoxia Inducible Factor (Hif) Alpha Subunit With In Vitro Nanomola Affinities.
J. Med. Chem. V. 57 8657 2014
PubMed-ID: 25166285  |  Reference-DOI: 10.1021/JM5011258

(-) Compounds

Molecule 1 - TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
    ChainsA, D, G, J
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPCDFDUET-1
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneTCEB2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymELONGIN 18 KDA SUBUNIT,ELONGIN-B,ELOB,RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT B,SIII P18
 
Molecule 2 - TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
    ChainsB, E, H, K
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPCDFDUET-1
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneTCEB1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymELONGIN 15 KDA SUBUNIT,ELONGIN-C,ELOC,RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT C,SIII P15
 
Molecule 3 - VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
    ChainsC, F, I, L
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPHAT4
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneVHL
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROTEIN G7,PVHL

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit ABCDEFGHIJKL
Biological Unit 1 (1x)ABC         
Biological Unit 2 (1x)   DEF      
Biological Unit 3 (1x)      GHI   
Biological Unit 4 (1x)         JKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
13JG4Ligand/Ion(4R)-1-(3,3-DIMETHYLBUTANOYL)-4-HYDROXY-N-[4-(1,3-OXAZOL-5-YL)BENZYL]-L-PROLINAMIDE
2CAS12Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
13JG1Ligand/Ion(4R)-1-(3,3-DIMETHYLBUTANOYL)-4-HYDROXY-N-[4-(1,3-OXAZOL-5-YL)BENZYL]-L-PROLINAMIDE
2CAS3Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
13JG1Ligand/Ion(4R)-1-(3,3-DIMETHYLBUTANOYL)-4-HYDROXY-N-[4-(1,3-OXAZOL-5-YL)BENZYL]-L-PROLINAMIDE
2CAS3Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
13JG1Ligand/Ion(4R)-1-(3,3-DIMETHYLBUTANOYL)-4-HYDROXY-N-[4-(1,3-OXAZOL-5-YL)BENZYL]-L-PROLINAMIDE
2CAS3Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
Biological Unit 4 (2, 4)
No.NameCountTypeFull Name
13JG1Ligand/Ion(4R)-1-(3,3-DIMETHYLBUTANOYL)-4-HYDROXY-N-[4-(1,3-OXAZOL-5-YL)BENZYL]-L-PROLINAMIDE
2CAS3Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP C:88 , TYR C:98 , PRO C:99 , ARG C:107 , ILE C:109 , HIS C:110 , SER C:111 , TYR C:112 , HIS C:115 , TRP C:117 , HOH C:434 , ARG L:182binding site for residue 3JG C 301
2AC2SOFTWARETRP F:88 , TYR F:98 , PRO F:99 , ARG F:107 , ILE F:109 , HIS F:110 , SER F:111 , HIS F:115 , TRP F:117binding site for residue 3JG F 301
3AC3SOFTWARETRP I:88 , TYR I:98 , PRO I:99 , ARG I:107 , ILE I:109 , HIS I:110 , SER I:111 , TYR I:112 , HIS I:115 , TRP I:117binding site for residue 3JG I 301
4AC4SOFTWARETRP L:88 , TYR L:98 , PRO L:99 , ARG L:107 , ILE L:109 , HIS L:110 , SER L:111 , TYR L:112 , HIS L:115 , TRP L:117binding site for residue 3JG L 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4W9C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4W9C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W9C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W9C)

(-) Exons   (0, 0)

(no "Exon" information available for 4W9C)

(-) 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:103
                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeee...hhhhhhhhhhhhhh.hhh.eeeee..ee......................eeeeeeeee..ee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 4w9c A   1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEcGFTSQTARPQAPATVGLAFRADDTFEALcIEPFSSPPELPDVM 103
                                    10        20        30        40        50        60        70        80        90       100   
                                                                                      60-CAS                       89-CAS          

Chain B from PDB  Type:PROTEIN  Length:86
                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeeehhhhh.hhhhhhhhh.eee....hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 4w9c B  17 MYVKLISSDGHEFIVKREHALTSGTIKAMLSNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC 112
                                    26        36        46||      66        76        86        96       106      
                                                         47|                                                      
                                                          58                                                      

Chain C from PDB  Type:PROTEIN  Length:141
                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeee.....eeeeee.....eee........eeeeeee...eeeeee.......ee................eeeeee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w9c C  62 VLRSVNSREPSQVIFcNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLT 202
                                    71     |  81        91       101       111       121       131       141       151       161       171       181       191       201 
                                          77-CAS                                                                                                                         

Chain D from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeee...hhhhhhhhhhhhhh.hhh.eeeee..ee......................eeeeeee....................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4w9c D   1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEcGFTSQTARPQAPATVGLAFRADTFEALcIEPFSSPPELPDVM 103
                                    10        20        30        40        50        60        70        80||     |91       101  
                                                                                      60-CAS               81|     |              
                                                                                                            83     |              
                                                                                                                  89-CAS          

Chain E from PDB  Type:PROTEIN  Length:88
                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeeehhhhh.hhhhhhhhh...eee....hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 4w9c E  17 MYVKLISSDGHEFIVKREHALTSGTIKAMLSGTNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC 112
                                    26        36        46 ||     64        74        84        94       104        
                                                          48|                                                       
                                                           57                                                       

Chain F from PDB  Type:PROTEIN  Length:144
                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeeeee.....eeeeee.....eee........eeeeeee...eeeeee.......ee..........hhhhh.eeeeee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4w9c F  62 VLRSVNSREPSQVIFcNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQER 205
                                    71     |  81        91       101       111       121       131       141       151       161       171       181       191       201    
                                          77-CAS                                                                                                                            

Chain G from PDB  Type:PROTEIN  Length:103
                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeee...hhhhhhhhhhhhhh.hhh.eeeee..ee......................eeeeeeeee..ee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 4w9c G   1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEcGFTSQTARPQAPATVGLAFRADDTFEALcIEPFSSPPELPDVM 103
                                    10        20        30        40        50        60        70        80        90       100   
                                                                                      60-CAS                       89-CAS          

Chain H from PDB  Type:PROTEIN  Length:88
                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeeehhhhh.hhhhhhhhhh..eee....hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 4w9c H  17 MYVKLISSDGHEFIVKREHALTSGTIKAMLSGTNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC 112
                                    26        36        46 ||     64        74        84        94       104        
                                                          48|                                                       
                                                           57                                                       

Chain I from PDB  Type:PROTEIN  Length:143
                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeee.....eeeeee.....eee........eeeeeee...eeeeee.......ee................eeeeee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w9c I  62 VLRSVNSREPSQVIFcNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQE 204
                                    71     |  81        91       101       111       121       131       141       151       161       171       181       191       201   
                                          77-CAS                                                                                                                           

Chain J from PDB  Type:PROTEIN  Length:103
                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeee...hhhhhhhhhhhhhh.hhh.eeeee..ee......................eeeeeeeee..ee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 4w9c J   1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEcGFTSQTARPQAPATVGLAFRADDTFEALcIEPFSSPPELPDVM 103
                                    10        20        30        40        50        60        70        80        90       100   
                                                                                      60-CAS                       89-CAS          

Chain K from PDB  Type:PROTEIN  Length:88
                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....eeeeehhhhh.hhhhhhhhh..eee....hhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 4w9c K  16 MMYVKLISSDGHEFIVKREHALTSGTIKAMLSTNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC 112
                                    25        35        45 ||     64        74        84        94       104        
                                                          47|                                                       
                                                           57                                                       

Chain L from PDB  Type:PROTEIN  Length:143
                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeee.....eeeeee.....eee........eeeeeee...eeeeee.......ee................eeeeee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w9c L  62 VLRSVNSREPSQVIFcNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQE 204
                                    71     |  81        91       101       111       121       131       141       151       161       171       181       191       201   
                                          77-CAS                                                                                                                           

   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4W9C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W9C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W9C)

(-) Gene Ontology  (39, 58)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ELOB_HUMAN | Q153701lm8 1lqb 1vcb 2c9w 2izv 2jz3 2ma9 3dcg 3zkj 3zng 3zrc 3zrf 3ztc 3ztd 3zun 4ajy 4awj 4b95 4b9k 4bks 4bkt 4n9f 4w9d 4w9e 4w9f 4w9g 4w9h 4w9i 4w9j 4w9k 4w9l 4wqo 5bo4 5lli 5n4w 5t35
        ELOC_HUMAN | Q153691lm8 1lqb 1vcb 2c9w 2izv 2ma9 3dcg 3zkj 3zng 3zrc 3zrf 3ztc 3ztd 3zun 4ajy 4awj 4b95 4b9k 4bks 4bkt 4n9f 4w9d 4w9e 4w9f 4w9g 4w9h 4w9i 4w9j 4w9k 4w9l 4wqo 5bo4 5lli 5n4w 5t35
        VHL_HUMAN | P403371lm8 1lqb 1vcb 3zrc 3zrf 3ztc 3ztd 3zun 4ajy 4awj 4b95 4b9k 4bks 4bkt 4w9d 4w9e 4w9f 4w9g 4w9h 4w9i 4w9j 4w9k 4w9l 4wqo 5lli 5n4w 5t35

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4W9C)