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(-) Description

Title :  THE REFINED STRUCTURE OF MONOMERIC DIPHTHERIA TOXIN AT 2.3 ANGSTROMS RESOLUTION
 
Authors :  M. J. Bennett, D. Eisenberg
Date :  21 Mar 94  (Deposition) - 31 Jul 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Bennett, D. Eisenberg
Refined Structure Of Monomeric Diphtheria Toxin At 2. 3 A Resolution.
Protein Sci. V. 3 1464 1994
PubMed-ID: 7833808
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIPHTHERIA TOXIN
    Chains: A, B
    Engineered: YES
    Organism Scientific: CORYNEPHAGE BETA
    Organism Taxid: 10703

 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
1APU2Ligand/IonADENYLYL-3'-5'-PHOSPHO-URIDINE-3'-MONOPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:21 , GLY A:22 , LYS A:24 , GLY A:34 , ILE A:35 , GLN A:36 , PRO A:38 , THR A:42 , GLY A:44 , PHE A:53 , TYR A:54 , TYR A:65 , TRP A:153 , SER A:446 , ARG A:458 , HOH A:538 , HOH A:539 , HOH A:586 , HOH A:588 , HOH A:590 , HOH A:667BINDING SITE FOR RESIDUE APU A 901
2AC2SOFTWAREHIS B:21 , GLY B:22 , LYS B:24 , TYR B:27 , ILE B:31 , GLY B:34 , ILE B:35 , GLN B:36 , THR B:42 , GLY B:44 , ASN B:45 , TYR B:54 , TYR B:65 , TRP B:153 , SER B:446 , ARG B:458 , HOH B:906 , HOH B:951 , HOH B:953 , HOH B:955 , HOH B:975 , HOH B:1003 , HOH B:1075BINDING SITE FOR RESIDUE APU B 901
3CATAUTHORHIS A:21 , TYR A:65 , GLU A:148 , SER A:446 , ARG A:458CATALYTIC SITE IN CHAIN A
4CBTAUTHORHIS B:21 , TYR B:65 , GLU B:148 , SER B:446 , ARG B:458CATALYTIC SITE IN CHAIN B

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:186 -A:201
2A:461 -A:471
3B:186 -B:201
4B:461 -B:471

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MDT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MDT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MDT)

(-) Exons   (0, 0)

(no "Exon" information available for 1MDT)

(-) 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:523
 aligned with DTX_CORBE | P00588 from UniProtKB/Swiss-Prot  Length:567

    Alignment length:535
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562     
            DTX_CORBE    33 GADDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQKPKSGTQGNYDDDWKGFYSTDNKYDAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGTEEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYEYMAQACAGNRVRRSVGSSLSCINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKTTAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNFVESIINLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKITAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVGNGVHANLHVAFHRSSSEKIHSNEISSDSIGVLGYQKTVDHTKVNSKLSLFFEIKS 567
               SCOP domains d1mdta2 A:1-187 Diphtheria toxin, N-terminal domain                                                                                                                                        ------------d1mdta3 A:200-380 Diphtheria toxin, middle domain                                                                                                                                    d1mdta1 A:381-535 Diphtheria toxin, C-terminal domain                                                                                                       SCOP domains
               CATH domains 1mdtA01 A:1-187 Diphtheria Toxin, domain 1                                                                                                                                                 ------------1mdtA02 A:200-379 Diphtheria toxin, middle domain                                                                                                                                   1mdtA03 A:380-534  [code=2.60.40.700, no name defined]                                                                                                     - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee.eeeeeee.....hhhhh...................eeee..hhhhhhhh............eeeeeee..eeeeeee....hhhhhhhh.......hhhhh..hhhhhhhh....eeeeeee.......eeeee...hhhh.eeeeeee.........hhhhhhhhhhh.------------......hhhhhhhhhhhhhhhhh.hhhhhhhhh.......hhhhhhhhhhhhhhh.....hhhhhhhhh......hhhhhhhhhhhhhh..hhhhh.hhhhhhhh.....hhhhh...........hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh............eee..eeeee......eee.....eeeeeeeeee........eeeee.............eeee..eeeeeeeeee...eeeeee...........eeeeeeeee..............eeeeeeeeeee..eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mdt A   1 GADDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQKPKSGTQGNYDDDWKGFYSTDNKYDAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGTEEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYEYMAQACA------------SCINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKTTAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNFVESIINLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKITAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVGNGVHANLHVAFHRSSSEKIHSNEISSDSIGVLGYQKTVDHTKVNSKLSLFFEIKS 535
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      |  -       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530     
                                                                                                                                                                                                                    187          200                                                                                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:523
 aligned with DTX_CORBE | P00588 from UniProtKB/Swiss-Prot  Length:567

    Alignment length:535
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562     
            DTX_CORBE    33 GADDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQKPKSGTQGNYDDDWKGFYSTDNKYDAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGTEEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYEYMAQACAGNRVRRSVGSSLSCINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKTTAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNFVESIINLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKITAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVGNGVHANLHVAFHRSSSEKIHSNEISSDSIGVLGYQKTVDHTKVNSKLSLFFEIKS 567
               SCOP domains d1mdtb2 B:1-187 Diphtheria toxin, N-terminal domain                                                                                                                                        ------------d1mdtb3 B:200-380 Diphtheria toxin, middle domain                                                                                                                                    d1mdtb1 B:381-535 Diphtheria toxin, C-terminal domain                                                                                                       SCOP domains
               CATH domains 1mdtB01 B:1-187 Diphtheria Toxin, domain 1                                                                                                                                                 ------------1mdtB02 B:200-379 Diphtheria toxin, middle domain                                                                                                                                   1mdtB03 B:380-534  [code=2.60.40.700, no name defined]                                                                                                     - CATH domains
           Pfam domains (1) Diphtheria_C-1mdtB01 B:1-187                                                                                                                                                               ------------Diphtheria_T-1mdtB05 B:200-379                                                                                                                                                      -Diphtheria_R-1mdtB03 B:381-534                                                                                                                            - Pfam domains (1)
           Pfam domains (2) Diphtheria_C-1mdtB02 B:1-187                                                                                                                                                               ------------Diphtheria_T-1mdtB06 B:200-379                                                                                                                                                      -Diphtheria_R-1mdtB04 B:381-534                                                                                                                            - Pfam domains (2)
         Sec.struct. author ...........eeee.eeeeeee.....hhhhh...................eeee..hhhhhhhh............eeeeeee..eeeeeee....hhhhhhhh.......hhhhh..hhhhhhhh....eeeeeee.......eeeee...hhhh.eeeeeee.........hhhhhhhhhhh.------------......hhhhhhhhhhhhhhhhh.hhhhhhhhh.......hhhhhhhhhhhhhhh.....hhhhhhhhh......hhhhhhhhhhhhhh..hhhhh.hhhhhhhh.....hhhhh...........hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh............eee..eeeee......eee.....eeeeeeeeee........eeeee.............eeee..eeeeeeeeee...eeeeee...........eeeeeeeee..............eeeeeeeeeee..eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mdt B   1 GADDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQKPKSGTQGNYDDDWKGFYSTDNKYDAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGTEEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYEYMAQACA------------SCINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKTTAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNFVESIINLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKITAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVGNGVHANLHVAFHRSSSEKIHSNEISSDSIGVLGYQKTVDHTKVNSKLSLFFEIKS 535
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      |  -       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530     
                                                                                                                                                                                                                    187          200
   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, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: ADP-ribosyl (56)
(-)
Clan: no clan defined [family: Diphtheria_R] (4)
(-)
Clan: no clan defined [family: Diphtheria_T] (4)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DTX_CORBE | P00588)
molecular function
    GO:0047286    NAD+-diphthamide ADP-ribosyltransferase activity    Catalysis of the reaction: peptide diphthamide + NAD+ = peptide N-(ADP-D-ribosyl)diphthamide + niacinamide.
    GO:0008320    protein transmembrane transporter activity    Enables the transfer of a protein from one side of a membrane to the other.
    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:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0071806    protein transmembrane transport    The directed movement of a protein across a membrane by means of some agent such as a transporter or pore.
cellular component
    GO:0030669    clathrin-coated endocytic vesicle membrane    The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
    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:0030666    endocytic vesicle membrane    The lipid bilayer surrounding an endocytic vesicle.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DTX_CORBE | P00588: 1ddt 1dtp 1f0l 1sgk 1tox 1xdt 4ae0 4ae1

(-) Related Entries Specified in the PDB File

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