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(-) Description

Title :  METAL ION AND LIGAND BINDING OF INTEGRIN
 
Authors :  W. Xia, T. A. Springer
Date :  01 Oct 14  (Deposition) - 03 Dec 14  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Cell Adhesion-Fibronectin Receptor, Cell Adhesion-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Xia, T. A. Springer
Metal Ion And Ligand Binding Of Integrin Alpha 5 Beta 1.
Proc. Natl. Acad. Sci. Usa V. 111 17863 2014
PubMed-ID: 25475857  |  Reference-DOI: 10.1073/PNAS.1420645111

(-) Compounds

Molecule 1 - INTEGRIN ALPHA-5
    ChainsA
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK 293
    Expression System CommonHUMAN
    Expression System Taxid9606
    FragmentUNP RESIDUES 42-493
    GeneITGA5, FNRA
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCD49 ANTIGEN-LIKE FAMILY MEMBER E,FIBRONECTIN RECEPTOR SUBUNIT ALPHA,INTEGRIN ALPHA-F,VLA-5
 
Molecule 2 - INTEGRIN BETA-1
    ChainsB
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK 293
    Expression System CommonHUMAN
    Expression System Taxid9606
    FragmentUNP RESIDUES 21-465
    GeneITGB1, FNRB, MDF2, MSK12
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFIBRONECTIN RECEPTOR SUBUNIT BETA,GLYCOPROTEIN IIA,GPIIA, VLA-4 SUBUNIT BETA
 
Molecule 3 - GLY-ARG-GLY-ASP-SER-PRO
    ChainsC
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 30)

Asymmetric/Biological Unit (5, 30)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CA6Ligand/IonCALCIUM ION
3MAN5Ligand/IonALPHA-D-MANNOSE
4MG1Ligand/IonMAGNESIUM ION
5NAG16Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:239 , SER A:241 , ASP A:243 , THR A:245 , ASP A:247 , HOH A:621binding site for residue CA A 501
02AC2SOFTWAREASP A:293 , ASN A:295 , ASP A:297 , LEU A:299 , ASP A:301 , HOH A:601binding site for residue CA A 502
03AC3SOFTWAREASP A:360 , ASP A:362 , ASP A:364 , TYR A:366 , ASP A:368 , HOH A:608 , HOH A:623binding site for residue CA A 503
04AC4SOFTWAREASP A:424 , ASP A:426 , ASN A:428 , TYR A:430 , ASP A:432 , HOH A:610binding site for residue CA A 504
05AC5SOFTWARESER B:132 , SER B:134 , GLU B:229 , HOH B:605 , HOH B:606 , ASP C:5003binding site for residue MG B 501
06AC6SOFTWARESER B:134 , ASP B:137 , ASP B:138 , HOH B:614 , HOH B:680binding site for residue CA B 502
07AC7SOFTWAREGLU B:169 , ASN B:224 , ASP B:226 , PRO B:228 , GLU B:229binding site for residue CA B 503
08AC8SOFTWAREPRO A:15 , GLY A:16 , LYS A:41 , ASN A:43 , LEU A:50 , GLN A:51binding site for Poly-Saccharide residues NAG A 514 through MAN A 517 bound to ASN A 43
09AC9SOFTWAREASN A:141binding site for Mono-Saccharide NAG A 520 bound to ASN A 141
10AD1SOFTWAREASN A:256 , TYR A:259 , SER A:277binding site for Poly-Saccharide residues NAG A 512 through NAG A 513 bound to ASN A 256
11AD2SOFTWARESER A:241 , ASN A:266 , ASP A:269binding site for Poly-Saccharide residues NAG A 518 through NAG A 519 bound to ASN A 266
12AD3SOFTWAREALA A:222 , TYR A:226 , TYR A:261 , SER A:272 , LEU A:273 , ASN A:275 , MAN A:509 , HOH A:616 , HOH A:671binding site for Poly-Saccharide residues NAG A 505 through MAN A 508 bound to ASN A 275
13AD4SOFTWAREASN B:192 , ARG B:220 , HOH B:669binding site for Mono-Saccharide NAG B 510 bound to ASN B 192
14AD5SOFTWAREASN B:249binding site for Poly-Saccharide residues NAG B 504 through NAG B 505 bound to ASN B 249
15AD6SOFTWAREASP B:137 , ASN B:343binding site for Mono-Saccharide NAG B 509 bound to ASN B 343
16AD7SOFTWAREGLY B:384 , ASN B:386binding site for Poly-Saccharide residues NAG B 506 through NAG B 507 bound to ASN B 386
17AD8SOFTWARELYS B:382 , ASN B:383 , ASN B:397binding site for Mono-Saccharide NAG B 508 bound to ASN B 397
18AD9SOFTWAREARG A:220 , GLN A:221 , ALA A:222 , SER A:223 , BMA A:507 , HOH A:674binding site for Poly-Saccharide residues MAN A 509 through MAN A 511

(-) SS Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1A:58 -A:67
2A:115 -A:135
3A:151 -A:164
4B:7 -B:25
5B:15 -B:444
6B:18 -B:44
7B:28 -B:55
8B:187 -B:193
9B:241 -B:281
10B:381 -B:395
11B:415 -B:442

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln B:95 -Pro B:96
2Met B:173 -Pro B:174

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WK2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WK2)

(-) Exons   (0, 0)

(no "Exon" information available for 4WK2)

(-) 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
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..........eeee.......eeeeee..............eeeeee.....eee......................ee.........eeee..eeeeee...ee............eeeeee....eeeee....................eeee.....eeeee.hhhhhh.eeeeehhhhhhhh.............ee....hhhhh.......eeee........eeeeee.hhhhhh.eeeee......eeeeee...........eeee........eeeeee...eee.....eee..eeeee.ee..ee.....eeee...........eeeee........eeeeee.........eeeee............eee................eeeee........eeeeeehhh.eeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4wk2 A    1 FNLDAEAPAVLSGPPGSFFGFSVEFYRPGTDGVSVLVGAPKANTSQPGVLQGGAVYLCPWGAQCTPIEFDSKGSRLLESSLSSEGEEPVEYKSLQWFGATVRAHGSSILACAPLYSWRTEKEPLSDPVGTCYLSTDNFTRILEYAPCRSDFSWAAGQGYCQGGFSAEFTKTGRVVLGGPGSYFWQGQILSATQEQIAESYYPEYLINLVQGQLQTRQASSIYDDSYLGYSVAVGEFSGDDTEDFVAGVPKGNLTYGYVTILNGSDIRSLYNFSGEQMASYFGYAVAATDVNGDGLDDLLVGAPLLMDRTPDGRPQEVGRVYVYLQHPAGIEPTPTLTLTGHDEFGRFGSSLTPLGDLDQDGYNDVAIGAPFGGETQQGVVFVFPGGPGGLGSKPSQVLQPLWAASHTPDFFGSALRGGRDLDGNGYPDLIVGSFGVDKAVVYRGRPVV  452
                                    10        20        30        40        50        60 ||     73        83||      94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444        
                                                                                        62|                84|                                                                                                                                                                                                                                                                                                                                                                              
                                                                                         66                 86                                                                                                                                                                                                                                                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:427
                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhh...eee..........eeehhhhhh.............eeeeee........hhhhh..ee..eeeeeee....eeeeeeee......eeeeeeee.hhhhhhhhhhh.hhhhhhhhhhhhh...eeeeeeee...........hhhhhhh.............eeeeeeee.hhhhhhhhhh............hhhhhhhhhhhh.........eeeeeeee.......hhhhhhh..........ee..ee.........hhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhh.eeeee......eeeeeeee.hhh.eee.hhh.ee.......eeeeeeeeee........eeeeeee......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4wk2 B    5 NRCLKANAKSCGECIQAGPNCGWCTNSTFLSARCDDLEALKKKGCPPDDIENPRGSKDIKKNKNVTNKLKPEDITQIQPQQLVLRLRSGEPQTFTLKFKRAEDYPIDLYYLMDLSYSMKDDLENVKSLGTDLMNEMRRITSDFRIGFGSFVEKTVMPYISTTPAKLRNPCTSEQNCTTPFSYKNVLSLTNKGEVFNELVGKQRISGNLDSPEGGFDAIMQVAVCGSLIGWRNVTRLLVFSTDAGFHFAGDGKLGGIVLPNDGQCHLENNMYTMSHYYDYPSIAHLVQKLSENNIQTIFAVTEEFQPVYKELKNLIPKSAVGTLSANSSNVIQLIIDAYNSLSSEVILENGKLSEGVTISYKSYCKNGVNGTGENGRKCSNISIGDEVQFEISITSNKCPKKDSDSFKIRPLGFTEEVEVILQYICEC  444
                                    14        24        34|       50        60        70      ||87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       
                                                        34|                                  77|                                                                                                                                                                                                                                                                                                                                                                       
                                                         41                                   85                                                                                                                                                                                                                                                                                                                                                                       

Chain C from PDB  Type:PROTEIN  Length:6
                                       
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                4wk2 C 5000 GRGDSP 5005

   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 4WK2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WK2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WK2)

(-) Gene Ontology  (149, 181)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ITA5_HUMAN | P086483vi3 3vi4 4wjk 4wk0 4wk4
        ITB1_HUMAN | P055561k11 1lha 3g9w 3t9k 3vi3 3vi4 4dx9 4wjk 4wk0 4wk4

(-) Related Entries Specified in the PDB File

4wjk 4wk0 4wk4