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(-) Description

Title :  THE ACTIVE SITE BASE CONTROLS COFACTOR REACTIVITY IN ESCHERICHIA COLI AMINE OXIDASE : X-RAY CRYSTALLOGRAPHIC STUDIES WITH MUTATIONAL VARIANTS
 
Authors :  J. M. Murray, C. M. Wilmot, C. G. Saysell, J. Jaeger, P. F. Knowles, S. E. Phillips, M. J. Mcpherson
Date :  15 Mar 99  (Deposition) - 24 Aug 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Copper, Tpq, Periplasmic, Catalytic Base Mutant (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. M. Murray, C. G. Saysell, C. M. Wilmot, W. S. Tambyrajah, J. Jaeger, P. F. Knowles, S. E. Phillips, M. J. Mcpherson
The Active Site Base Controls Cofactor Reactivity In Escherichia Coli Amine Oxidase: X-Ray Crystallographic Studies With Mutational Variants.
Biochemistry V. 38 8217 1999
PubMed-ID: 10387067  |  Reference-DOI: 10.1021/BI9900469
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COPPER AMINE OXIDASE
    Cellular LocationPERIPLASM
    ChainsA, B
    EC Number1.4.3.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPKK233-3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneMAOA
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CU2Ligand/IonCOPPER (II) ION
3TPQ2Mod. Amino Acid5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETPQ A:466 , HIS A:524 , HIS A:526 , HIS A:689 , HOH A:1574BINDING SITE FOR RESIDUE CU A 801
2AC2SOFTWARELYS A:133 , ASP A:533 , LEU A:534 , ASP A:535 , ASP A:678 , ALA A:679 , HOH A:949BINDING SITE FOR RESIDUE CA A 802
3AC3SOFTWAREGLU A:573 , TYR A:667 , ASP A:670 , GLU A:672 , HOH A:975BINDING SITE FOR RESIDUE CA A 803
4AC4SOFTWARETPQ B:466 , HIS B:524 , HIS B:526 , HIS B:689BINDING SITE FOR RESIDUE CU B 801
5AC5SOFTWARELYS B:133 , ASP B:533 , LEU B:534 , ASP B:535 , ASP B:678 , ALA B:679 , HOH B:970BINDING SITE FOR RESIDUE CA B 802
6AC6SOFTWAREGLU B:573 , TYR B:667 , ASP B:670 , GLU B:672 , HOH B:999BINDING SITE FOR RESIDUE CA B 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QAK)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:696 -Pro A:697
2Trp B:696 -Pro B:697

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric/Biological Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_AMO_ECOLI_001 *K42EAMO_ECOLI  ---  ---A/BK12E
2UniProtVAR_AMO_ECOLI_002 *L59IAMO_ECOLI  ---  ---A/BL29I
   * ID not provided by source

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPPER_AMINE_OXID_1PS01164 Copper amine oxidase topaquinone signature.AMO_ECOLI485-498
 
  2A:455-468
B:455-468
2COPPER_AMINE_OXID_2PS01165 Copper amine oxidase copper-binding site signature.AMO_ECOLI714-727
 
  2A:684-697
B:684-697

(-) Exons   (0, 0)

(no "Exon" information available for 1QAK)

(-) 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:720
 aligned with AMO_ECOLI | P46883 from UniProtKB/Swiss-Prot  Length:757

    Alignment length:720
                                    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       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755
            AMO_ECOLI    36 HMVPMDKTLKEFGADVQWDDYAQLFTLIKDGAYVKVKPGAQTAIVNGQPLALQVPVVMKDNKAWVSDTFINDVFQSGLDQTFQVEKRPHPLNALTADEIKQAVEIVKASADFKPNTRFTEISLLPPDKEAVWAFALENKPVDQPRKADVIMLDGKHIIEAVVDLQNNKLLSWQPIKDAHGMVLLDDFASVQNIINNSEEFAAAVKKRGITDAKKVITTPLTVGYFDGKDGLKQDARLLKVISYLDVGDGNYWAHPIENLVAVVDLEQKKIVKIEEGPVVPVPMTARPFDGRDRVAPAVKPMQIIEPEGKNYTITGDMIHWRNWDFHLSMNSRVGPMISTVTYNDNGTKRKVMYEGSLGGMIVPYGDPDIGWYFKAYLDSGDYGMGTLTSPIARGKDAPSNAVLLNETIADYTGVPMEIPRAIAVFERYAGPEYKHQEMGQPNVSTERRELVVRWISTVGNYDYIFDWIFHENGTIGIDAGATGIEAVKGVKAKTMHDETAKDDTRYGTLIDHNIVGTTHQHIYNFRLDLDVDGENNSLVAMDPVVKPNTAGGPRTSTMQVNQYNIGNEQDAAQKFDPGTIRLLSNPNKENRMGNPVSYQIIPYAGGTHPVAKGAQFAPDEWIYHRLSFMDKQLWVTRYHPGERFPEGKYPNRSTHDTGLGQYSKDNESLDNTDAVVWMTTGTTHVARAEEWPIMPTEWVHTLLKPWNFFDETPTLGALKK 755
               SCOP domains d1qaka4 A:6-90 Copper amine oxidase, domain N                                        d1qaka2 A:91-185 Copper amine oxidase, domains 1 and 2                                         d1qaka3 A:186-300 Copper amine oxidase, domains 1 and 2                                                            d1qaka1 A:301-725 Copper amine oxidase, domain 3                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1qakA01 A:6-84  [code=3.30.457.10, no name defined]                            -1qakA02 A:86-186  [code=3.10.450.40, no name defined]                                                1qakA04 A:187-292  [code=3.10.450.40, no name defined]                                                    ---------------------1qakA03 A:314-723 Copper amine oxidase, Domain 3                                                                                                                                                                                                                                                                                                                                                                          -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeehhhhhhhhh.eeeee....eeeeee..eeeee.....eeee..eeee.....eee..eeeee.hhhhhhhh...................hhhhhhhhhhhhhh........eeeeeeee..hhhhhhhhhhhh.......eeeeeeee..eeeeeeee....eeeeeee........hhhhhhhhhhhhhhhhhhhhhhhhh...hhh.eeeeee................eeeeeeee.....hhhhh....eeeeee....eeeeeee.................ee.......eee........................................................................hhhhhhh.......................................................................................................eee.........hhhhhh..eeeee..eeee.................................................hhhhhh...............................................hhhhhhhhhhhh..........................hhhhhhhh.....................hhhhh............................. Sec.struct. author
                 SAPs(SNPs) ------E----------------I------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COPPER_AMINE_O-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COPPER_AMINE_O---------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qak A   6 HMVPMDKTLKEFGADVQWDDYAQLFTLIKDGAYVKVKPGAQTAIVNGQPLALQVPVVMKDNKAWVSDTFINDVFQSGLDQTFQVEKRPHPLNALTADEIKQAVEIVKASADFKPNTRFTEISLLPPDKEAVWAFALENKPVDQPRKADVIMLDGKHIIEAVVDLQNNKLLSWQPIKDAHGMVLLDDFASVQNIINNSEEFAAAVKKRGITDAKKVITTPLTVGYFDGKDGLKQDARLLKVISYLDVGDGNYWAHPIENLVAVVDLEQKKIVKIEEGPVVPVPMTARPFDGRDRVAPAVKPMQIIEPEGKNYTITGDMIHWRNWDFHLSMNSRVGPMISTVTYNDNGTKRKVMYEGSLGGMIVPYGDPDIGWYFKAYLASGDYGMGTLTSPIARGKDAPSNAVLLNETIADYTGVPMEIPRAIAVFERYAGPEYKHQEMGQPNVSTERRELVVRWISTVGNyDYIFDWIFHENGTIGIDAGATGIEAVKGVKAKTMHDETAKDDTRYGTLIDHNIVGTTHQHIYNFRLDLDVDGENNSLVAMDPVVKPNTAGGPRTSTMQVNQYNIGNEQDAAQKFDPGTIRLLSNPNKENRMGNPVSYQIIPYAGGTHPVAKGAQFAPDEWIYHRLSFMDKQLWVTRYHPGERFPEGKYPNRSTHDTGLGQYSKDNESLDNTDAVVWMTTGTTHVARAEEWPIMPTEWVHTLLKPWNFFDETPTLGALKK 725
                                    15        25        35        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       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      466-TPQ                                                                                                                                                                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:722
 aligned with AMO_ECOLI | P46883 from UniProtKB/Swiss-Prot  Length:757

    Alignment length:722
                                    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       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755  
            AMO_ECOLI    36 HMVPMDKTLKEFGADVQWDDYAQLFTLIKDGAYVKVKPGAQTAIVNGQPLALQVPVVMKDNKAWVSDTFINDVFQSGLDQTFQVEKRPHPLNALTADEIKQAVEIVKASADFKPNTRFTEISLLPPDKEAVWAFALENKPVDQPRKADVIMLDGKHIIEAVVDLQNNKLLSWQPIKDAHGMVLLDDFASVQNIINNSEEFAAAVKKRGITDAKKVITTPLTVGYFDGKDGLKQDARLLKVISYLDVGDGNYWAHPIENLVAVVDLEQKKIVKIEEGPVVPVPMTARPFDGRDRVAPAVKPMQIIEPEGKNYTITGDMIHWRNWDFHLSMNSRVGPMISTVTYNDNGTKRKVMYEGSLGGMIVPYGDPDIGWYFKAYLDSGDYGMGTLTSPIARGKDAPSNAVLLNETIADYTGVPMEIPRAIAVFERYAGPEYKHQEMGQPNVSTERRELVVRWISTVGNYDYIFDWIFHENGTIGIDAGATGIEAVKGVKAKTMHDETAKDDTRYGTLIDHNIVGTTHQHIYNFRLDLDVDGENNSLVAMDPVVKPNTAGGPRTSTMQVNQYNIGNEQDAAQKFDPGTIRLLSNPNKENRMGNPVSYQIIPYAGGTHPVAKGAQFAPDEWIYHRLSFMDKQLWVTRYHPGERFPEGKYPNRSTHDTGLGQYSKDNESLDNTDAVVWMTTGTTHVARAEEWPIMPTEWVHTLLKPWNFFDETPTLGALKKDK 757
               SCOP domains d1qakb4 B:6-90 Copper amine oxidase, domain N                                        d1qakb2 B:91-185 Copper amine oxidase, domains 1 and 2                                         d1qakb3 B:186-300 Copper amine oxidase, domains 1 and 2                                                            d1qakb1 B:301-727 Copper amine oxidase, domain 3                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1qakB01 B:6-84  [code=3.30.457.10, no name defined]                            -1qakB02 B:86-186  [code=3.10.450.40, no name defined]                                                1qakB04 B:187-292  [code=3.10.450.40, no name defined]                                                    ---------------------1qakB03 B:314-723 Copper amine oxidase, Domain 3                                                                                                                                                                                                                                                                                                                                                                          ---- CATH domains
           Pfam domains (1) Cu_amine_oxidN1-1qakB05 B:6-91                                                        --Cu_amine_oxidN2-1qakB01 B:94-180                                                       ----Cu_amine_oxidN3-1qakB03 B:185-287                                                                      -----------------Cu_amine_oxid-1qakB07 B:305-727                                                                                                                                                                                                                                                                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) Cu_amine_oxidN1-1qakB06 B:6-91                                                        --Cu_amine_oxidN2-1qakB02 B:94-180                                                       ----Cu_amine_oxidN3-1qakB04 B:185-287                                                                      -----------------Cu_amine_oxid-1qakB08 B:305-727                                                                                                                                                                                                                                                                                                                                                                                                         Pfam domains (2)
         Sec.struct. author .eeehhhhhhhhh.eeeee....eeeeee..eeeee.....eeee..eeee.....eee..eeeee.hhhhhhhh...................hhhhhhhhhhhhhhh.......eeeeeee...hhhhhhhhhhhh.......eeeeeeee..eeeeeeee....eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh...hhh.eeeeee................eeeeeeee.....hhhh.eeeeeeeeee....eeeeeee..........................eee........................................................................hhhhhhh.......................................................................................................eee.........hhhhhh..eeeee..eeee.................................................hhhhhh...............................................hhhhhhhhhhhh..........................hhhhhhh......................hhhhh.........................ee.... Sec.struct. author
                 SAPs(SNPs) ------E----------------I-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COPPER_AMINE_O-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COPPER_AMINE_O------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qak B   6 HMVPMDKTLKEFGADVQWDDYAQLFTLIKDGAYVKVKPGAQTAIVNGQPLALQVPVVMKDNKAWVSDTFINDVFQSGLDQTFQVEKRPHPLNALTADEIKQAVEIVKASADFKPNTRFTEISLLPPDKEAVWAFALENKPVDQPRKADVIMLDGKHIIEAVVDLQNNKLLSWQPIKDAHGMVLLDDFASVQNIINNSEEFAAAVKKRGITDAKKVITTPLTVGYFDGKDGLKQDARLLKVISYLDVGDGNYWAHPIENLVAVVDLEQKKIVKIEEGPVVPVPMTARPFDGRDRVAPAVKPMQIIEPEGKNYTITGDMIHWRNWDFHLSMNSRVGPMISTVTYNDNGTKRKVMYEGSLGGMIVPYGDPDIGWYFKAYLASGDYGMGTLTSPIARGKDAPSNAVLLNETIADYTGVPMEIPRAIAVFERYAGPEYKHQEMGQPNVSTERRELVVRWISTVGNyDYIFDWIFHENGTIGIDAGATGIEAVKGVKAKTMHDETAKDDTRYGTLIDHNIVGTTHQHIYNFRLDLDVDGENNSLVAMDPVVKPNTAGGPRTSTMQVNQYNIGNEQDAAQKFDPGTIRLLSNPNKENRMGNPVSYQIIPYAGGTHPVAKGAQFAPDEWIYHRLSFMDKQLWVTRYHPGERFPEGKYPNRSTHDTGLGQYSKDNESLDNTDAVVWMTTGTTHVARAEEWPIMPTEWVHTLLKPWNFFDETPTLGALKKDK 727
                                    15        25        35        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       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      466-TPQ                                                                                                                                                                                                                                                                 

   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  (3, 8)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (4, 8)

Asymmetric/Biological Unit

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (AMO_ECOLI | P46883)
molecular function
    GO:0052595    aliphatic-amine oxidase activity    Catalysis of the reaction: an aliphatic amine + H2O + O2 = an aldehyde + NH3 + hydrogen peroxide + H+.
    GO:0052594    aminoacetone:oxygen oxidoreductase(deaminating) activity    Catalysis of the reaction: aminoacetone + H2O + O2 = methylglyoxal + NH3 + hydrogen peroxide + H+.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0052596    phenethylamine:oxygen oxidoreductase (deaminating) activity    Catalysis of the reaction: phenylethylamine + O2 + H2O = phenylacetaldehyde + NH3 + hydrogen peroxide + H+.
    GO:0008131    primary amine oxidase activity    Catalysis of the reaction: a primary amine + H2O + O2 = an aldehyde + NH3 + hydrogen peroxide.
    GO:0048038    quinone binding    Interacting selectively and non-covalently with a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds.
    GO:0052593    tryptamine:oxygen oxidoreductase (deaminating) activity    Catalysis of the reaction: tryptamine + H2O + O2 = NH3 + indole acetaldehyde + hydrogen peroxide + H+.
biological process
    GO:0006559    L-phenylalanine catabolic process    The chemical reactions and pathways resulting in the breakdown of phenylalanine, 2-amino-3-phenylpropanoic acid.
    GO:0009308    amine metabolic process    The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0019607    phenylethylamine catabolic process    The chemical reactions and pathways resulting in the breakdown of phenylethylamine, an amine with pharmacological properties similar to those of amphetamine, occurs naturally as a neurotransmitter in the brain, and is present in chocolate and oil of bitter almonds.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        AMO_ECOLI | P468831d6u 1d6y 1d6z 1dyu 1jrq 1lvn 1oac 1qaf 1qal 1spu 2w0q 2wgq 2wo0 2wof 2woh

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QAK)