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(-) Description

Title :  TI(IV) BOUND HUMAN SERUM TRANSFERRIN
 
Authors :  M. Saxena, S. Sharma, N. Noinaj, T. B. Parks, A. D. Tinoco
Date :  24 Sep 15  (Deposition) - 27 Apr 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.68
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Synergistic Ion Complex, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. D. Tinoco, M. Saxena, S. Sharma, N. Noinaj, Y. Delgado, E. P. Quinones Gonzalez, S. E. Conklin, N. Zambrana, S. A. Loza-Rosas T. B. Parks
Unusual Synergism Of Transferrin And Citrate In The Regulation Of Ti(Iv) Speciation, Transport, And Toxicity.
J. Am. Chem. Soc. V. 138 5659 2016
PubMed-ID: 27070073  |  Reference-DOI: 10.1021/JACS.6B01966

(-) Compounds

Molecule 1 - SEROTRANSFERRIN
    Chains: A, B
    Engineered: YES
    Expression System: ORYZA SATIVA
    Expression System Common: RICE
    Expression System Taxid: 4530
    Gene: TF, PRO1400
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TRANSFERRIN,BETA-1 METAL-BINDING GLOBULIN,SIDEROPHILIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric Unit (3, 15)
No.NameCountTypeFull Name
14TI2Ligand/IonTITANIUM ION
2CIT11Ligand/IonCITRIC ACID
3CO32Ligand/IonCARBONATE ION
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
14TI1Ligand/IonTITANIUM ION
2CIT6Ligand/IonCITRIC ACID
3CO31Ligand/IonCARBONATE ION
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
14TI1Ligand/IonTITANIUM ION
2CIT5Ligand/IonCITRIC ACID
3CO31Ligand/IonCARBONATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:426 , ARG A:456 , THR A:457 , TYR A:517 , 4TI A:707 , CO3 A:708binding site for residue CIT A 701
02AC2SOFTWARETYR A:95 , ARG A:124 , SER A:125 , TYR A:188 , LYS A:206binding site for residue CIT A 702
03AC3SOFTWAREARG A:456 , GLY A:516 , TYR A:517 , THR A:518binding site for residue CIT A 703
04AC4SOFTWAREARG A:124 , GLY A:187 , TYR A:188 , SER A:189binding site for residue CIT A 704
05AC5SOFTWAREGLU A:338 , LYS A:599 , ARG B:602 , HIS B:606binding site for residue CIT A 705
06AC6SOFTWAREHIS A:578 , ARG A:581 , GLU A:654binding site for residue CIT A 706
07AC7SOFTWARETYR A:426 , TYR A:517 , CIT A:701 , CO3 A:708binding site for residue 4TI A 707
08AC8SOFTWARETYR A:426 , THR A:452 , ARG A:456 , THR A:457 , ALA A:458 , GLY A:459 , TYR A:517 , CIT A:701 , 4TI A:707binding site for residue CO3 A 708
09AC9SOFTWARETYR B:426 , ARG B:456 , THR B:457 , TYR B:517 , CIT B:702 , 4TI B:706 , CO3 B:707binding site for residue CIT B 701
10AD1SOFTWAREARG B:456 , TYR B:515 , GLY B:516 , TYR B:517 , THR B:518 , CIT B:701binding site for residue CIT B 702
11AD2SOFTWARETYR B:95 , ARG B:124 , SER B:125 , TYR B:188 , LYS B:206binding site for residue CIT B 703
12AD3SOFTWAREARG B:124 , PHE B:186 , GLY B:187 , TYR B:188 , SER B:189binding site for residue CIT B 704
13AD4SOFTWARESER A:348 , HIS A:349 , HIS A:350 , SER B:348 , HIS B:349 , HIS B:350binding site for residue CIT B 705
14AD5SOFTWARETYR B:426 , TYR B:517 , CIT B:701 , CO3 B:707binding site for residue 4TI B 706
15AD6SOFTWARETYR B:426 , THR B:452 , ARG B:456 , THR B:457 , ALA B:458 , GLY B:459 , TYR B:517 , CIT B:701 , 4TI B:706binding site for residue CO3 B 707

(-) SS Bonds  (38, 38)

Asymmetric Unit
No.Residues
1A:9 -A:48
2A:19 -A:39
3A:118 -A:194
4A:137 -A:331
5A:158 -A:174
6A:161 -A:179
7A:171 -A:177
8A:227 -A:241
9A:339 -A:596
10A:345 -A:377
11A:355 -A:368
12A:402 -A:674
13A:418 -A:637
14A:450 -A:523
15A:474 -A:665
16A:484 -A:498
17A:495 -A:506
18A:563 -A:577
19A:615 -A:620
20B:9 -B:48
21B:19 -B:39
22B:118 -B:194
23B:137 -B:331
24B:158 -B:174
25B:161 -B:179
26B:171 -B:177
27B:227 -B:241
28B:339 -B:596
29B:345 -B:377
30B:355 -B:368
31B:402 -B:674
32B:418 -B:637
33B:450 -B:523
34B:474 -B:665
35B:484 -B:498
36B:495 -B:506
37B:563 -B:577
38B:615 -B:620

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ala A:73 -Pro A:74
2Glu A:141 -Pro A:142
3Lys A:144 -Pro A:145
4Ala B:73 -Pro B:74
5Glu B:141 -Pro B:142
6Lys B:144 -Pro B:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DYH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DYH)

(-) Exons   (0, 0)

(no "Exon" information available for 5DYH)

(-) 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 A from PDB  Type:PROTEIN  Length:677
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhh.....eeehhhhhhhhhh....eeeeeeee.........eeeeeeeee.....hhhhh....eee........hhhhhhhhhhhh.....hhhhhhhhhh..ee........hhhhhh.............hhhhhhhhhhhh....eeeee.hhhhhhh.hhhhhh.eeee.....eee.hhhhhh..eeee..eeeee....hhhhhhhhhhhhhhhhh.........................eeee.....hhhhhhhhhhhhhhhhhhhh............eeeee.hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh....eeeehhhhhhhhhhh..eeeeeee..............eeeeeeee..............eeee........hhhhhhhhhhhhh.........eee.......hhhhh..................hhhhhhhhhhhhh..eeeee.hhhhhh.............hhh.eeee.....eee.hhh.....eee...eeee...hhhhhhhhhhhhhhhhh...........................eeee.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dyh A   3 DKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFYYAVAVVKKDSGFQMNQLRGKKSCHTGLGRSAGWNIPIGLLYCDLPEPRKPLEKAVANFFSGSCAPCADGTDFPQLCQLCPGCGCSTLNQYFGYSGAFKCLKDGAGDVAFVKHSTIFENLANKADRDQYELLCLDNTRKPVDEYKDCHLAQVPSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLGYEYVTAIRNLREGTCPEAPTDECKPVKWCALSHHERLKCDEWSVNSVGKIECVSAETTEDCIAKIMNGEADAMSLDGGFVYIAGKCGLVPVLAENYNKSDNCEDTPEAGYFAIAVVKKSASDLTWDNLKGKKSCHTAVGRTAGWNIPMGLLYNKINHCRFDEFFSEGCAPGSKKDSSLCKLCMGSGLNLCEPNNKEGYYGYTGAFRCLVEKGDVAFVKHQTVPQNTGGKNPDPWAKNLNEKDYELLCLDGTRKPVEEYANCHLARAPNHAVVTRKDKEACVHKILRQQQHLFGSNVTDCSGNFCLFRSETKDLLFRDDTVCLAKLHDRNTYEKYLGEEYVKAVGNLRKCSTSSLLEACTFRRP 679
                                    12        22        32        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       572       582       592       602       612       622       632       642       652       662       672       


Chain B from PDB  Type:PROTEIN  Length:677
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhh.....eeehhhhhhhhhh....eeeeeeee.........eeeeeeeee.....hhhhh....eee........hhhhhhhhhhhh.....hhhhhhhhhh..ee........hhhhhh.............hhhhhhhhhhhh....eeeee.hhhhhhh.hhhhhh.eeee.....eee.hhhhhh..eeee..eeeee....hhhhhhhhhhhhhhhhh.........................eeee.....hhhhhhhhhhhhhhhhhhhh............eeeee.hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh....eeehhhhhhhhhhh..eeeeeee..............eeeeeeee..............eeee........hhhhhhhhhhhhh.........eee.......hhhhh....hhhhh.........hhhhhhhhhhhhh..eeeee.hhhhhh.............hhh.eeee.....eee.hhh.....eee...eeeehhhhhhhhhhhhhhhhhhhh...........................eeee.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dyh B   3 DKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFYYAVAVVKKDSGFQMNQLRGKKSCHTGLGRSAGWNIPIGLLYCDLPEPRKPLEKAVANFFSGSCAPCADGTDFPQLCQLCPGCGCSTLNQYFGYSGAFKCLKDGAGDVAFVKHSTIFENLANKADRDQYELLCLDNTRKPVDEYKDCHLAQVPSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLGYEYVTAIRNLREGTCPEAPTDECKPVKWCALSHHERLKCDEWSVNSVGKIECVSAETTEDCIAKIMNGEADAMSLDGGFVYIAGKCGLVPVLAENYNKSDNCEDTPEAGYFAIAVVKKSASDLTWDNLKGKKSCHTAVGRTAGWNIPMGLLYNKINHCRFDEFFSEGCAPGSKKDSSLCKLCMGSGLNLCEPNNKEGYYGYTGAFRCLVEKGDVAFVKHQTVPQNTGGKNPDPWAKNLNEKDYELLCLDGTRKPVEEYANCHLARAPNHAVVTRKDKEACVHKILRQQQHLFGSNVTDCSGNFCLFRSETKDLLFRDDTVCLAKLHDRNTYEKYLGEEYVKAVGNLRKCSTSSLLEACTFRRP 679
                                    12        22        32        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       572       582       592       602       612       622       632       642       652       662       672
   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 5DYH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DYH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DYH)

(-) Gene Ontology  (36, 36)

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  5dyh
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  TRFE_HUMAN | P02787
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 Related Entries

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        TRFE_HUMAN | P02787: 1a8e 1a8f 1b3e 1bp5 1btj 1d3k 1d4n 1dtg 1fqe 1fqf 1jqf 1n7w 1n7x 1n84 1oqg 1oqh 1ryo 1suv 2hau 2hav 2o7u 2o84 3fgs 3qyt 3s9l 3s9m 3s9n 3skp 3v83 3v89 3v8x 3ve1 4h0w 4x1b 4x1d

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