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(-) Description

Title :  CRYSTAL STRUCTURE OF DROSOPHILA 3,4-DIHYDROXYPHENYLALANINE DECARBOXYLASE
 
Authors :  Q. Han, H. Ding, H. Robinson, B. M. Christensen, J. Li
Date :  05 Oct 09  (Deposition) - 02 Feb 10  (Release) - 02 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Plp Dependent Protein, Alpha Beta Protein, Alternative Splicing, Catecholamine Biosynthesis, Decarboxylase, Lyase, Polymorphism, Pyridoxal Phosphate, Cg10697-Pb Isoform B (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Q. Han, H. Ding, H. Robinson, B. M. Christensen, J. Li
Crystal Structure And Substrate Specificity Of Drosophila 3, 4-Dihydroxyphenylalanine Decarboxylase
Plos One V. 5 E8826 2010
PubMed-ID: 20098687  |  Reference-DOI: 10.1371/JOURNAL.PONE.0008826

(-) Compounds

Molecule 1 - AROMATIC-L-AMINO-ACID DECARBOXYLASE
    ChainsA, B
    EC Number4.1.1.28
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTYB
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneCG10697, DDC
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    Other DetailsHYPODERM ISOFORM
    SynonymAADC, DOPA DECARBOXYLASE, DDC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:1 , GLU A:2 , HOH A:781 , TYR B:366 , ASN B:370 , HOH B:599BINDING SITE FOR RESIDUE GOL A 476

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K40)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:308 -Asp A:309
2Phe B:308 -Asp B:309

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 10)

Asymmetric/Biological Unit (5, 10)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_DDC_DROME_002 *K197NDDC_DROME  ---  ---A/BK162N
2UniProtVAR_DDC_DROME_003 *V264MDDC_DROME  ---  ---A/BV229M
3UniProtVAR_DDC_DROME_004 *R390MDDC_DROME  ---  ---A/BR355M
4UniProtVAR_DDC_DROME_005 *S428FDDC_DROME  ---  ---A/BS393F
5UniProtVAR_DDC_DROME_006 *S489ADDC_DROME  ---  ---A/BS454A
   * ID not provided by source

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DDC_GAD_HDC_YDCPS00392 DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site.DDC_DROME330-351
 
  2A:295-316
B:295-316

(-) Exons   (0, 0)

(no "Exon" information available for 3K40)

(-) 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:448
 aligned with DDC_DROME | P05031 from UniProtKB/Swiss-Prot  Length:510

    Alignment length:475
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505     
            DDC_DROME    36 MEAPEFKDFAKTMVDFIAEYLENIRERRVLPEVKPGYLKPLIPDAAPEKPEKWQDVMQDIERVIMPGVTHWHSPKFHAYFPTANSYPAIVADMLSGAIACIGFTWIASPACTELEVVMMDWLGKMLELPAEFLACSGGKGGGVIQGTASESTLVALLGAKAKKLKEVKELHPEWDEHTILGKLVGYCSDQAHSSVERAGLLGGVKLRSVQSENHRMRGAALEKAIEQDVAEGLIPFYAVVTLGTTNSCAFDYLDECGPVGNKHNLWIHVDAAYAGSAFICPEYRHLMKGIESADSFNFNPHKWMLVNFDCSAMWLKDPSWVVNAFNVDPLYLKHDMQGSAPDYRHWQIPLGRRFRALKLWFVLRLYGVENLQAHIRRHCNFAKQFGDLCVADSRFELAAEINMGLVCFRLKGSNERNEALLKRINGRGHIHLVPAKIKDVYFLRMAICSRFTQSEDMEYSWKEVSAAADEMEQEQ 510
               SCOP domains d3k40a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 3k40A01 A:1-81 dopa decarboxylase, N-terminal domain                             3k40A02 A:82-376 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                                                   3k40A03 A:377-475 Aspartate Aminotransferase, domain 1                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh.........hhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh..hhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhheeeeee...hhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhh.eeeehhhhhh......eeeee.hhhhh---------------------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.......eeeeee..hhhhhhhhhhhhhhhh....eeeee..eeeeeee......hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------N------------------------------------------------------------------M-----------------------------------------------------------------------------------------------------------------------------M-------------------------------------F------------------------------------------------------------A--------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DDC_GAD_HDC_YDC       --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k40 A   1 MEAPEFKDFAKTMVDFIAEYLENIRERRVLPEVKPGYLKPLIPDAAPEKPEKWQDVMQDIERVIMPGVTHWHSPKFHAYFPTANSYPAIVADMLSGAIACIGFTWIASPACTELEVVMMDWLGKMLELPAEFLACSGGKGGGVIQGTASESTLVALLGAKAKKLKEVKELHPEWDEHTILGKLVGYCSDQAHSSVERAGLLGGVKLRSVQSENHRMRGAALEKAIEQDVAEGLIPFYAVVTLGTTNSCAFDYLDECGPVGNKHNLWIHVDAAYAGSAFICPEYRHLMKGIESADSFNFNPHkWMLVNFDCSAMWLKDPSWV---------------------------PLGRRFRALKLWFVLRLYGVENLQAHIRRHCNFAKQFGDLCVADSRFELAAEINMGLVCFRLKGSNERNEALLKRINGRGHIHLVPAKIKDVYFLRMAICSRFTQSEDMEYSWKEVSAAADEMEQEQ 475
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 |     310       320|        -         -       350       360       370       380       390       400       410       420       430       440       450       460       470     
                                                                                                                                                                                                                                                                                                                                       302-LLP            321                         349                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:448
 aligned with DDC_DROME | P05031 from UniProtKB/Swiss-Prot  Length:510

    Alignment length:475
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505     
            DDC_DROME    36 MEAPEFKDFAKTMVDFIAEYLENIRERRVLPEVKPGYLKPLIPDAAPEKPEKWQDVMQDIERVIMPGVTHWHSPKFHAYFPTANSYPAIVADMLSGAIACIGFTWIASPACTELEVVMMDWLGKMLELPAEFLACSGGKGGGVIQGTASESTLVALLGAKAKKLKEVKELHPEWDEHTILGKLVGYCSDQAHSSVERAGLLGGVKLRSVQSENHRMRGAALEKAIEQDVAEGLIPFYAVVTLGTTNSCAFDYLDECGPVGNKHNLWIHVDAAYAGSAFICPEYRHLMKGIESADSFNFNPHKWMLVNFDCSAMWLKDPSWVVNAFNVDPLYLKHDMQGSAPDYRHWQIPLGRRFRALKLWFVLRLYGVENLQAHIRRHCNFAKQFGDLCVADSRFELAAEINMGLVCFRLKGSNERNEALLKRINGRGHIHLVPAKIKDVYFLRMAICSRFTQSEDMEYSWKEVSAAADEMEQEQ 510
               SCOP domains d3k40b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 3k40B01 B:1-81 dopa decarboxylase, N-terminal domain                             3k40B02 B:82-376 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                                                   3k40B03 B:377-475 Aspartate Aminotransferase, domain 1                                              CATH domains
           Pfam domains (1) ----------------------------------Pyridoxal_deC-3k40B01 B:35-411                                                                                                                                                                                                                                                                                                                                                           ---------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------Pyridoxal_deC-3k40B02 B:35-411                                                                                                                                                                                                                                                                                                                                                           ---------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh.........hhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh..hhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh.eeeeee...hhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhh...eeeeeeee..........hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhh.eeeehhhhhh......eeeee......---------------------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.......eeeeee..hhhhhhhhhhhhhhhh....eeeee..eeeeeee......hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------N------------------------------------------------------------------M-----------------------------------------------------------------------------------------------------------------------------M-------------------------------------F------------------------------------------------------------A--------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DDC_GAD_HDC_YDC       --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k40 B   1 MEAPEFKDFAKTMVDFIAEYLENIRERRVLPEVKPGYLKPLIPDAAPEKPEKWQDVMQDIERVIMPGVTHWHSPKFHAYFPTANSYPAIVADMLSGAIACIGFTWIASPACTELEVVMMDWLGKMLELPAEFLACSGGKGGGVIQGTASESTLVALLGAKAKKLKEVKELHPEWDEHTILGKLVGYCSDQAHSSVERAGLLGGVKLRSVQSENHRMRGAALEKAIEQDVAEGLIPFYAVVTLGTTNSCAFDYLDECGPVGNKHNLWIHVDAAYAGSAFICPEYRHLMKGIESADSFNFNPHkWMLVNFDCSAMWLKDPSWV---------------------------PLGRRFRALKLWFVLRLYGVENLQAHIRRHCNFAKQFGDLCVADSRFELAAEINMGLVCFRLKGSNERNEALLKRINGRGHIHLVPAKIKDVYFLRMAICSRFTQSEDMEYSWKEVSAAADEMEQEQ 475
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 |     310       320|        -         -       350       360       370       380       390       400       410       420       430       440       450       460       470     
                                                                                                                                                                                                                                                                                                                                       302-LLP            321                         349                                                                                                                              

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DDC_DROME | P05031)
molecular function
    GO:0004058    aromatic-L-amino-acid decarboxylase activity    Catalysis of the reaction: L-amino acid + H+ = R-H + CO2.
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
    GO:0048085    adult chitin-containing cuticle pigmentation    Establishment of the adult pattern of pigmentation in the chitin-containing cuticle of an organism. An example of this is the adult cuticle pigmentation process in Drosophila melanogaster.
    GO:0007615    anesthesia-resistant memory    The memory process that results in the formation of consolidated memory resistant to disruption of the patterned activity of the brain, without requiring protein synthesis.
    GO:0019752    carboxylic acid metabolic process    The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
    GO:0042423    catecholamine biosynthetic process    The chemical reactions and pathways resulting in the formation of any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine.
    GO:0006584    catecholamine metabolic process    The chemical reactions and pathways involving any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine.
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0007619    courtship behavior    The behavioral interactions between organisms for the purpose of attracting sexual partners.
    GO:0048066    developmental pigmentation    The developmental process that results in the deposition of coloring matter in an organism, tissue or cell.
    GO:0006585    dopamine biosynthetic process from tyrosine    The chemical reactions and pathways resulting in the formation of dopamine (3,4-dihydroxyphenylethylamine) from L-tyrosine, via the metabolic precursor 3,4-dihydroxy-L-phenylalanine (L-dopa). Dopamine is a catecholamine neurotransmitter and a metabolic precursor of norepinephrine and epinephrine.
    GO:0008062    eclosion rhythm    The timing of the emergence of the adult fly from its pupal case, which usually occurs at dawn.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0007611    learning or memory    The acquisition and processing of information and/or the storage and retrieval of this information over time.
    GO:0007616    long-term memory    The memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation.
    GO:0048082    regulation of adult chitin-containing cuticle pigmentation    Any process that modulates the frequency, rate or extent of establishment of the adult pattern of pigmentation in the cuticle of an organism.
    GO:0009611    response to wounding    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
    GO:0006587    serotonin biosynthetic process from tryptophan    The chemical reactions and pathways resulting in the formation from tryptophan of serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties.
    GO:0040040    thermosensory behavior    Behavior that is dependent upon the sensation of temperature.
    GO:0043052    thermotaxis    The directed movement of a motile cell or organism in response to a temperature gradient. Movement may be towards either a higher or lower temperature.
    GO:0035220    wing disc development    Progression of the wing disc over time, from its initial formation through to its metamorphosis to form adult structures including the wing hinge, wing blade and pleura.

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