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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ALPHA 1,6-FUCOSYLTRANSFERASE, FUT8
 
Authors :  N. Taniguchi, H. Ihara, A. Nakagawa
Date :  07 Feb 06  (Deposition) - 26 Dec 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym. Unit :  X
Biol. Unit 1:  X  (1x)
Biol. Unit 2:  X  (2x)
Keywords :  Fut8, Fucosyltransferase, Glycosyltransferase, N-Glycan, Core Fucose, Sh3 Domain, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Ihara, Y. Ikeda, S. Toma, X. Wang, T. Suzuki, J. Gu, E. Miyoshi, T. Tsukihara, K. Honke, A. Matsumoto, A. Nakagawa, N. Taniguchi
Crystal Structure Of Mammalian {Alpha}1, 6-Fucosyltransferase, Fut8
Glycobiology V. 17 455 2007
PubMed-ID: 17172260  |  Reference-DOI: 10.1093/GLYCOB/CWL079

(-) Compounds

Molecule 1 - ALPHA-(1,6)-FUCOSYLTRANSFERASE
    ChainsX
    EC Number2.4.1.68
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPACGP67B
    Expression System StrainSF21
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentRESIDUES 68-575
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit X
Biological Unit 1 (1x)X
Biological Unit 2 (2x)X

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2DE0)

(-) Sites  (0, 0)

(no "Site" information available for 2DE0)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1X:204 -X:266
2X:212 -X:230
3X:218 -X:222
4X:465 -X:472

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro X:305 -Leu X:306
2His X:357 -Pro X:358

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_033537T267KFUT8_HUMANPolymorphism35949016XT267K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_033537T267KFUT8_HUMANPolymorphism35949016XT267K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_033537T267KFUT8_HUMANPolymorphism35949016XT267K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GT23PS51659 Glycosyltransferase family 23 (GT23) domain profile.FUT8_HUMAN206-493  1X:206-493
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GT23PS51659 Glycosyltransferase family 23 (GT23) domain profile.FUT8_HUMAN206-493  1X:206-493
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GT23PS51659 Glycosyltransferase family 23 (GT23) domain profile.FUT8_HUMAN206-493  2X:206-493

(-) Exons   (7, 7)

Asymmetric Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003945861bENSE00001422457chr14:65877840-65878711872FUT8_HUMAN-00--
1.4ENST000003945864ENSE00001383814chr14:66028055-66028484430FUT8_HUMAN1-68680--
1.5ENST000003945865ENSE00001679723chr14:66082696-66082811116FUT8_HUMAN68-107400--
1.6ENST000003945866ENSE00001741486chr14:66082929-66083091163FUT8_HUMAN107-161551X:108-16154
1.8ENST000003945868ENSE00000941037chr14:66096210-66096324115FUT8_HUMAN161-199391X:161-19939
1.9aENST000003945869aENSE00000658487chr14:66135961-66136198238FUT8_HUMAN200-279801X:200-27980
1.10ENST0000039458610ENSE00000658486chr14:66188493-66188739247FUT8_HUMAN279-361831X:279-36183
1.11ENST0000039458611ENSE00000658485chr14:66190865-66191041177FUT8_HUMAN361-420601X:361-420 (gaps)60
1.12ENST0000039458612ENSE00001796173chr14:66199949-66200099151FUT8_HUMAN420-470511X:420-47051
1.13cENST0000039458613cENSE00001254535chr14:66208811-662099611151FUT8_HUMAN471-5751051X:471-572102

(-) 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 X from PDB  Type:PROTEIN  Length:460
 aligned with FUT8_HUMAN | Q9BYC5 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:465
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567     
           FUT8_HUMAN   108 LGKDHEILRRRIENGAKELWFFLQSELKKLKNLEGNELQRHADEFLLDLGHHERSIMTDLYYLSQTDGAGDWREKEAKDLTELVQRRITYLQNPKDCSKAKKLVCNINKGCGYGCQLHHVVYCFMIAYGTQRTLILESQNWRYATGGWETVFRPVSETCTDRSGISTGHWSGEVKDKNVQVVELPIVDSLHPRPPYLPLAVPEDLADRLVRVHGDPAVWWVSQFVKYLIRPQPWLEKEIEEATKKLGFKHPVIGVHVRRTDKVGTEAAFHPIEEYMVHVEEHFQLLARRMQVDKKRVYLATDDPSLLKEAKTKYPNYEFISDNSISWSAGLHNRYTENSLRGVILDIHFLSQADFLVCTFSSQVCRVAYEIMQTLHPDASANFHSLDDIYYFGGQNAHNQIAIYAHQPRTADEIPMEPGDIIGVAGNHWDGYSKGVNRKLGRTGLYPSYKVREKIETVKYPTYPE 572
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeeee.....hhhhhhhhhhhhhhhhhhh..eeeee.........hhhhh......................hhhhhh.eeee.hhhhh..........ee..hhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....eeeeee...-----.....hhhhhhhhhhhhhhhhhh.......eeeeee.hhhhhhhhhhhh...eee........hhhhhhh..hhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhh.........eee.............eeee..................eeeeeee....eeeeee.....eeeee...eee...ee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------K----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------GT23  PDB: X:206-493 UniProt: 206-493                                                                                                                                                                                                                                                           ------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: X:108-161 UniProt: 107-161 [INCOMPLETE]---------------------------------------------------------------------------------------------------------------------Exon 1.10  PDB: X:279-361 UniProt: 279-361                                         ----------------------------------------------------------Exon 1.12  PDB: X:420-470 UniProt: 420-470         Exon 1.13c  PDB: X:471-572 UniProt: 471-575 [INCOMPLETE]                                               Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.8  PDB: X:161-199               Exon 1.9a  PDB: X:200-279 UniProt: 200-279                                      ---------------------------------------------------------------------------------Exon 1.11  PDB: X:361-420 (gaps) UniProt: 361-420           -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2de0 X 108 LGKDHEILRRRIENGAKELWFFLQSELKKLKNLEGNELQRHADEFLLDLGHHERSIMTDLYYLSQTDGAGDWREKEAKDLTELVQRRITYLQNPKDCSKAKKLVCNINKGCGYGCQLHHVVYCFMIAYGTQRTLILESQNWRYATGGWETVFRPVSETCTDRSGISTGHWSGEVKDKNVQVVELPIVDSLHPRPPYLPLAVPEDLADRLVRVHGDPAVWWVSQFVKYLIRPQPWLEKEIEEATKKLGFKHPVIGVHVRRT-----EAAFHPIEEYMVHVEEHFQLLARRMQVDKKRVYLATDDPSLLKEAKTKYPNYEFISDNSISWSAGLHNRYTENSLRGVILDIHFLSQADFLVCTFSSQVCRVAYEIMQTLHPDASANFHSLDDIYYFGGQNAHNQIAIYAHQPRTADEIPMEPGDIIGVAGNHWDGYSKGVNRKLGRTGLYPSYKVREKIETVKYPTYPE 572
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367     | 377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567     
                                                                                                                                                                                                                                                                                             367   373                                                                                                                                                                                                       

   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 2DE0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DE0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DE0)

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)
Chain X   (FUT8_HUMAN | Q9BYC5)
molecular function
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    GO:0046921    alpha-(1->6)-fucosyltransferase activity    Catalysis of the transfer of an L-fucosyl group from GDP-beta-L-fucose to an acceptor molecule to form an alpha-(1->6) linkage.
    GO:0008424    glycoprotein 6-alpha-L-fucosyltransferase activity    Catalysis of the reaction: N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-acetyl-beta-D-glucosaminyl}-L-asparagine + GDP-L-fucose = N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-[alpha-L-fucosyl-(1->6)]-N-acetyl-beta-D-glucosaminyl}asparagine + GDP + H(+).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0046368    GDP-L-fucose metabolic process    The chemical reactions and pathways involving GDP-L-fucose, a substance composed of L-fucose in glycosidic linkage with guanosine diphosphate.
    GO:0042355    L-fucose catabolic process    The chemical reactions and pathways resulting in the breakdown of L-fucose (6-deoxy-Lgalactose).
    GO:0036071    N-glycan fucosylation    The process of transferring a fucosyl group to an N-glycan. An N-glycan is the carbohydrate portion of an N-glycoprotein when attached to a nitrogen from asparagine or arginine side-chains.
    GO:0006491    N-glycan processing    The conversion of N-linked glycan (N = nitrogen) structures from the initially transferred oligosaccharide to a mature form, by the actions of glycosidases and glycosyltransferases. The early processing steps are conserved and play roles in glycoprotein folding and trafficking.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0007229    integrin-mediated signaling pathway    A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0009312    oligosaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.
    GO:0006487    protein N-linked glycosylation    A protein glycosylation process in which a carbohydrate or carbohydrate derivative unit is added to a protein via the N4 atom of peptidyl-asparagine, the omega-N of arginine, or the N1' atom peptidyl-tryptophan.
    GO:0018279    protein N-linked glycosylation via asparagine    The glycosylation of protein via the N4 atom of peptidyl-asparagine forming N4-glycosyl-L-asparagine; the most common form is N-acetylglucosaminyl asparagine; N-acetylgalactosaminyl asparagine and N4 glucosyl asparagine also occur. This modification typically occurs in extracellular peptides with an N-X-(ST) motif. Partial modification has been observed to occur with cysteine, rather than serine or threonine, in the third position; secondary structure features are important, and proline in the second or fourth positions inhibits modification.
    GO:0006486    protein glycosylation    A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins.
    GO:0033578    protein glycosylation in Golgi    The addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid in any compartment of the Golgi apparatus.
    GO:0043112    receptor metabolic process    The chemical reactions and pathways involving a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:1900407    regulation of cellular response to oxidative stress    Any process that modulates the frequency, rate or extent of cellular response to oxidative stress.
    GO:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0007585    respiratory gaseous exchange    The process of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
    GO:0007179    transforming growth factor beta receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0032580    Golgi cisterna membrane    The lipid bilayer surrounding any of the thin, flattened compartments that form the central portion of the Golgi complex.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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