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(-) Description

Title :  E2-RING EXPANSION OF THE NEDD8 CASCADE CONFERS SPECIFICITY TO CULLIN MODIFICATION.
 
Authors :  D. T. Huang, O. Ayrault, H. W. Hunt, A. M. Taherbhoy, D. M. Duda, D. C. Scot L. A. Borg, G Neale, P. J. Murray, M. F. Roussel, B. A. Schulman
Date :  22 Dec 08  (Deposition) - 17 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, Atp-Binding, Cell Cycle, Nucleotide-Binding, Ubl Conjugation Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. T. Huang, O. Ayrault, H. W. Hunt, A. M. Taherbhoy, D. M. Duda, D. C. Scott, L. A. Borg, G. Neale, P. J. Murray, M. F. Roussel, B. A. Schulman
E2-Ring Expansion Of The Nedd8 Cascade Confers Specificity To Cullin Modification
Mol. Cell V. 33 483 2009
PubMed-ID: 19250909  |  Reference-DOI: 10.1016/J.MOLCEL.2009.01.011

(-) Compounds

Molecule 1 - NEDD8-ACTIVATING ENZYME E1 CATALYTIC SUBUNIT
    ChainsA
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX4T1
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUBIQUITIN-ACTIVATING ENZYME E1C, RESIDUE 368-463
    GeneE1C, UBA3, UBE1C
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN-LIKE MODIFIER-ACTIVATING ENZYME 3, UBIQUITIN- ACTIVATING ENZYME 3, NEDD8-ACTIVATING ENZYME E1C, UBIQUITIN- ACTIVATING ENZYME E1C
 
Molecule 2 - NEDD8-CONJUGATING ENZYME UBE2F
    ChainsB
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX4T1
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneNCE2, UBE2F
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN-CONJUGATING ENZYME E2 F, NEDD8 PROTEIN LIGASE UBE2F, NEDD8 CARRIER PROTEIN UBE2F, NEDD8-CONJUGATING ENZYME 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3FN1)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:50 -B:50

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FN1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FN1)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBE2F_HUMAN35-174  1B:35-174
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBE2F_HUMAN105-120  1B:105-120

(-) Exons   (13, 13)

Asymmetric/Biological Unit (13, 13)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000002729301cENSE00001841551chr2:238875597-238875774178UBE2F_HUMAN-00--
1.3ENST000002729303ENSE00000965342chr2:238881734-238881867134UBE2F_HUMAN1-40401B:26-4015
1.6ENST000002729306ENSE00001639741chr2:238896605-23889663430UBE2F_HUMAN40-50111B:40-5011
1.8ENST000002729308ENSE00001685506chr2:238903386-23890345166UBE2F_HUMAN50-72231B:50-7223
1.10cENST0000027293010cENSE00001722321chr2:238925208-23892527568UBE2F_HUMAN72-94231B:72-9423
1.11cENST0000027293011cENSE00001595446chr2:238933983-23893405371UBE2F_HUMAN95-118241B:95-11824
1.12bENST0000027293012bENSE00001722543chr2:238939197-23893925458UBE2F_HUMAN118-137201B:118-13720
1.13aENST0000027293013aENSE00001619260chr2:238940863-23894089533UBE2F_HUMAN138-148111B:138-14811
1.14cENST0000027293014cENSE00001638076chr2:238944519-23894458163UBE2F_HUMAN149-169211B:149-16921
1.15sENST0000027293015sENSE00001638496chr2:238949929-2389512361308UBE2F_HUMAN170-185161B:170-18516

2.1aENST000003610551aENSE00001864869chr3:69129559-6912948575UBA3_HUMAN1-770--
2.2aENST000003610552aENSE00001417479chr3:69129304-6912926342UBA3_HUMAN7-21150--
2.3aENST000003610553aENSE00000966869chr3:69127069-69126949121UBA3_HUMAN21-61410--
2.4aENST000003610554aENSE00001377164chr3:69124661-6912458181UBA3_HUMAN62-88270--
2.5aENST000003610555aENSE00001376644chr3:69120768-6912068683UBA3_HUMAN89-116280--
2.6ENST000003610556ENSE00000966872chr3:69117159-6911707981UBA3_HUMAN116-143280--
2.7aENST000003610557aENSE00000966873chr3:69113262-6911321944UBA3_HUMAN143-158160--
2.8ENST000003610558ENSE00000966874chr3:69112654-6911259065UBA3_HUMAN158-179220--
2.9ENST000003610559ENSE00000966875chr3:69112288-69112133156UBA3_HUMAN180-231520--
2.10ENST0000036105510ENSE00000966876chr3:69111330-69111228103UBA3_HUMAN232-266350--
2.11aENST0000036105511aENSE00000966877chr3:69111078-69110965114UBA3_HUMAN266-304390--
2.12ENST0000036105512ENSE00000966878chr3:69106460-6910640754UBA3_HUMAN304-322190--
2.13ENST0000036105513ENSE00001656120chr3:69105966-6910593037UBA3_HUMAN322-334130--
2.14ENST0000036105514ENSE00001685710chr3:69105844-6910576382UBA3_HUMAN334-361280--
2.15ENST0000036105515ENSE00001754233chr3:69105434-69105334101UBA3_HUMAN362-395341A:350-37425
2.16ENST0000036105516ENSE00001711956chr3:69105214-6910515164UBA3_HUMAN395-416221A:374-39522
2.17ENST0000036105517ENSE00001673741chr3:69105056-6910500255UBA3_HUMAN417-435191A:396-41419
2.18bENST0000036105518bENSE00001518240chr3:69104676-69103881796UBA3_HUMAN435-463291A:414-44128

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:92
 aligned with UBA3_HUMAN | Q8TBC4 from UniProtKB/Swiss-Prot  Length:463

    Alignment length:92
                                   380       390       400       410       420       430       440       450       460  
           UBA3_HUMAN   371 PQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHFT 462
               SCOP domains d3fn1a_ A: UBA3                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhh........eeeeee..eeeeeee..hhhhhhhhhhhhhh...........eeeee.......eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.15  PDB: A:350-374---------------------Exon 2.17          --------------------------- Transcript 2 (1)
           Transcript 2 (2) ------------------------Exon 2.16             ------------------Exon 2.18b  PDB: A:414-441   Transcript 2 (2)
                 3fn1 A 350 PQNIQFSPSAKLQEVLDYLTNSASLQmKSPAITATLEGKNRTLYmQSVTSIEERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHFT 441
                                   359       369      |379       389    |  399       409       419       429       439  
                                                    376-MSE           394-MSE                                           

Chain B from PDB  Type:PROTEIN  Length:160
 aligned with UBE2F_HUMAN | Q969M7 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:160
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185
          UBE2F_HUMAN    26 STRRVSVRDKLLVKEVAELEANLPCTCKVHFPDPNKLHCFQLTVTPDEGYYQGGKFQFETEVPDAYNMVPPKVKCLTKIWHPNITETGEICLSLLREHSIDGTGWAPTRTLKDVVWGLNSLFTDLLNFDDPLNIEAAEHHLRDKEDFRNKVDDYIKRYAR 185
               SCOP domains d3fn1b_ B: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh...eeee........eeeeee...........eeeeee..........eeee................hhhhh.............hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------UBIQUITIN_CONJUGAT_2  PDB: B:35-174 UniProt: 35-174                                                                                         ----------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------UBIQUITIN_CONJUG----------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3       -------------------------------Exon 1.10c  PDB: B:72-9Exon 1.11c  PDB: B:95-11-------------------Exon 1.13a Exon 1.14c           Exon 1.15s       Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.6   -------------------------------------------------------------------Exon 1.12b          ------------------------------------------------ Transcript 1 (2)
           Transcript 1 (3) ------------------------Exon 1.8  PDB: B:50-72 ----------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 3fn1 B  26 STRRVSVRDKLLVKEVAELEANLPCTCKVHFPDPNKLHCFQLTVTPDEGYYQGGKFQFETEVPDAYNMVPPKVKCLTKIWHPNITETGEICLSLLREHSIDGTGWAPTRTLKDVVWGLNSLFTDLLNFDDPLNIEAAEHHLRDKEDFRNKVDDYIKRYAR 185
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3FN1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FN1)

(-) Gene Ontology  (26, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UBA3_HUMAN | Q8TBC4)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0019781    NEDD8 activating enzyme activity    Catalysis of the initiation of the NEDD8 (RUB1) conjugation cascade.
    GO:0016881    acid-amino acid ligase activity    Catalysis of the ligation of an acid to an amino acid via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0016922    ligand-dependent nuclear receptor binding    Interacting selectively and non-covalently, in a ligand dependent manner, with a nuclear receptor protein.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0008641    small protein activating enzyme activity    Catalysis of the activation of small proteins, such as ubiquitin or ubiquitin-like proteins, through the formation of an ATP-dependent high-energy thiolester bond.
biological process
    GO:0038061    NIK/NF-kappaB signaling    The process in which a signal is passed on to downstream components within the cell through the NIK-dependent processing and activation of NF-KappaB. Begins with activation of the NF-KappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-Kappa B2 protein (p100) leading to p100 processing and release of an active NF-KappaB (p52).
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0007113    endomitotic cell cycle    A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell.
    GO:0000278    mitotic cell cycle    Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045116    protein neddylation    Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain B   (UBE2F_HUMAN | Q969M7)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0019788    NEDD8 transferase activity    Catalysis of the transfer of NEDD8 from one protein to another via the reaction X-NEDD8 + Y --> Y-NEDD8 + X, where both X-NEDD8 and Y-NEDD8 are covalent linkages.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0006301    postreplication repair    The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication. Includes pathways that remove replication-blocking lesions in conjunction with DNA replication.
    GO:0070534    protein K63-linked ubiquitination    A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is added to a protein. K63-linked ubiquitination does not target the substrate protein for degradation, but is involved in several pathways, notably as a signal to promote error-free DNA postreplication repair.
    GO:0045116    protein neddylation    Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UBA3_HUMAN | Q8TBC41r4m 1r4n 1tt5 1y8x 1yov 2lq7 2nvu 3dbh 3dbl 3dbr 3gzn 5jjm
        UBE2F_HUMAN | Q969M72edi 4gba

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3FN1)