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(-) Description

Title :  YTTERBIUM-BOUND HUMAN SERUM TRANSFERRIN
 
Authors :  M. Wang, H. Zhang, H. Sun
Date :  24 Nov 14  (Deposition) - 08 Apr 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferrin, Ytterbium, Ferric, Malonate, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Wang, T. P. Lai, L. Wang, H. Zhang, N. Yang, P. J. Sadler, H. Sun
"Anion Clamp" Allows Flexible Protein To Impose Coordinatio Geometry On Metal Ions
Chem. Commun. (Camb. ) V. 51 7867 2015
PubMed-ID: 25854324  |  Reference-DOI: 10.1039/C4CC09642H

(-) Compounds

Molecule 1 - SEROTRANSFERRIN
    Chains: A, B
    Organ: SERUM
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: YB-HTF,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, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MLI2Ligand/IonMALONATE ION
3YB2Ligand/IonYTTERBIUM (III) ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MLI1Ligand/IonMALONATE ION
3YB-1Ligand/IonYTTERBIUM (III) ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MLI1Ligand/IonMALONATE ION
3YB-1Ligand/IonYTTERBIUM (III) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:392 , TYR A:426 , TYR A:517 , HIS A:585 , MLI A:702binding site for residue YB A 701
2AC2SOFTWAREASP A:392 , TYR A:426 , THR A:452 , ARG A:456 , THR A:457 , ALA A:458 , GLY A:459 , TYR A:517 , HIS A:585 , YB A:701binding site for residue MLI A 702
3AC3SOFTWARECYS A:227 , LEU A:228 , ASP A:229 , ASP A:240 , HIS A:242 , HOH A:836binding site for residue GOL A 703
4AC4SOFTWAREASP B:392 , TYR B:426 , TYR B:517 , HIS B:585 , MLI B:702binding site for residue YB B 701
5AC5SOFTWAREASP B:392 , TYR B:426 , THR B:452 , ARG B:456 , THR B:457 , ALA B:458 , GLY B:459 , TYR B:517 , HIS B:585 , YB B:701binding site for residue MLI B 702
6AC6SOFTWARELEU B:228 , ASP B:229 , ASP B:240 , HIS B:242 , HOH B:835binding site for residue GOL B 703

(-) SS Bonds  (34, 34)

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:450 -A:523
14A:474 -A:665
15A:484 -A:498
16A:495 -A:506
17A:563 -A:577
18B:9 -B:48
19B:19 -B:39
20B:118 -B:194
21B:137 -B:331
22B:158 -B:174
23B:161 -B:179
24B:171 -B:177
25B:227 -B:241
26B:339 -B:596
27B:345 -B:377
28B:355 -B:368
29B:402 -B:674
30B:450 -B:523
31B:474 -B:665
32B:484 -B:498
33B:495 -B:506
34B:563 -B:577

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ala A:73 -Pro A:74
2Glu A:141 -Pro A:142
3Lys A:144 -Pro A:145
4Gly A:258 -Lys A:259
5Ala B:73 -Pro B:74
6Glu B:141 -Pro B:142
7Lys B:144 -Pro B:145
8Gly B:258 -Lys B:259

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X1D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X1D)

(-) Exons   (0, 0)

(no "Exon" information available for 4X1D)

(-) 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:658
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhh.....eeehhhhhhhhhh....eeeeeeeeee....ee.eeeeeeeee.....hhhhh...eeee........hhhhhhhhhhhh.....hhhhhhhh...eee........hhhhh..............hhhhhhhhhhhh....eeeee.hhhhhhh.hhhhhh.eeee.....ee...hhhhh..eeee..eeeee....hhhhhhhhhhhhhhhhh.........................eeee.....hhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh.....eeehhhhhhhhhhh..eeeeeee.......eeeeeeee...............eee........hhhhhhhhhhhhh..hhhhh...ee.......hhhhh....hhhhh.........hhhhhhhhhhhhh..eeeee.hhhhhh......hhhhhh.hhh.eeee.....eee..hhhhh..eee...eeeehhhhhhhhhhhhhhhhhhhh....................eee......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x1d A   3 DKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFYYAVAVVKKDSGFQMNQLRGKKSCHTGLGRSAGWNIPIGLLYCDLPEPRKPLEKAVANFFSGSCAPCADGTDFPQLCQLCPGCGCSTLNQYFGYSGAFKCLKDGAGDVAFVKHSTIFENLANKADRDQYELLCLDNTRKPVDEYKDCHLAQVPSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLGYEYVTAIRNLREGTCPECKPVKWCALSHHERLKCDEWSVNSVGKIECVSAETTEDCIAKIMNGEADAMSLDGGFVYIAGKCGLVPVLAENYNKPEAGYFAVAVVKKSASDLTWDNLKGKKSCHTAVGRTAGWNIPMGLLYNKINHCRFDEFFSEGCAPGSKKDSSLCKLCMGSGLNLCEPNNKEGYYGYTGAFRCLVEKGDVAFVKHQTVPQNTGGKNPDPWAKNLNEKDYELLCLDGTRKPVEEYANCHLARAPNHAVVTRKDKEACVHKILRQQQHLFGSNFCLFRSETKDLLFRDDTVCLAKLHDRNTYEKYLGEEYVKAVGNLRKCSTSSLLEACTFRRP 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||     347       357       367       377       387       397       407      |424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604      |621       631       641       651       661       671        
                                                                                                                                                                                                                                                                                                                                                                    333|                                                                        414|                                                                                                                                                                                          611|                                                            
                                                                                                                                                                                                                                                                                                                                                                     339                                                                         422                                                                                                                                                                                           619                                                            


Chain B from PDB  Type:PROTEIN  Length:658
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhh.....eeehhhhhhhhhh....eeeeeeee.........eeeeeeeee.....hhhhh...eeee........hhhhhhhhhhhh.....hhhhhhhh...eee........hhhhh..............hhhhhhhhhhhh....eeeee.hhhhhhh.hhhhhh.eeee.....ee...hhhhh..eeee..eeeee....hhhhhhhhhhhhhhhhh.........................eeee.....hhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh.....eeehhhhhhhhhhh..eeeeeee.......eeeeeeee...............eee........hhhhhhhhhhhhh..hhhhh...ee.......hhhhh....hhhhh.........hhhhhhhhhhhhh..eeeee.hhhhhh......hhhhhh.hhh.eeee.....eee..hhhhh..eee...eeeehhhhhhhhhhhhhhhhhhhh....................eee......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x1d B   3 DKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFYYAVAVVKKDSGFQMNQLRGKKSCHTGLGRSAGWNIPIGLLYCDLPEPRKPLEKAVANFFSGSCAPCADGTDFPQLCQLCPGCGCSTLNQYFGYSGAFKCLKDGAGDVAFVKHSTIFENLANKADRDQYELLCLDNTRKPVDEYKDCHLAQVPSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLGYEYVTAIRNLREGTCPECKPVKWCALSHHERLKCDEWSVNSVGKIECVSAETTEDCIAKIMNGEADAMSLDGGFVYIAGKCGLVPVLAENYNKPEAGYFAVAVVKKSASDLTWDNLKGKKSCHTAVGRTAGWNIPMGLLYNKINHCRFDEFFSEGCAPGSKKDSSLCKLCMGSGLNLCEPNNKEGYYGYTGAFRCLVEKGDVAFVKHQTVPQNTGGKNPDPWAKNLNEKDYELLCLDGTRKPVEEYANCHLARAPNHAVVTRKDKEACVHKILRQQQHLFGSNFCLFRSETKDLLFRDDTVCLAKLHDRNTYEKYLGEEYVKAVGNLRKCSTSSLLEACTFRRP 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||     347       357       367       377       387       397       407      |424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604      |621       631       641       651       661       671        
                                                                                                                                                                                                                                                                                                                                                                    333|                                                                        414|                                                                                                                                                                                          611|                                                            
                                                                                                                                                                                                                                                                                                                                                                     339                                                                         422                                                                                                                                                                                           619
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4X1D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X1D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X1D)

(-) Gene Ontology  (36, 36)

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 Related Entries

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

UniProtKB/Swiss-Prot
        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 5dyh

(-) Related Entries Specified in the PDB File

4x1b FERRIC BOUND HUMAN SERUM TRANSFERRIN