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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 :  1.78
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
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 42-493
    Gene: ITGA5, FNRA
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CD49 ANTIGEN-LIKE FAMILY MEMBER E,FIBRONECTIN RECEPTOR SUBUNIT ALPHA,INTEGRIN ALPHA-F,VLA-5
 
Molecule 2 - INTEGRIN BETA-1
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 21-465
    Gene: ITGB1, FNRB, MDF2, MSK12
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: FIBRONECTIN RECEPTOR SUBUNIT BETA,GLYCOPROTEIN IIA,GPIIA, VLA-4 SUBUNIT BETA
 
Molecule 3 - ARG-GLY-ASP
    Chains: C
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 25)

Asymmetric/Biological Unit (5, 25)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA6Ligand/IonCALCIUM ION
3MAN3Ligand/IonALPHA-D-MANNOSE
4MG1Ligand/IonMAGNESIUM ION
5NAG14Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:239 , SER A:241 , ASP A:243 , THR A:245 , ASP A:247 , HOH A:636binding site for residue CA A 501
02AC2SOFTWAREASP A:293 , ASN A:295 , ASP A:297 , LEU A:299 , ASP A:301 , HOH A:604binding site for residue CA A 502
03AC3SOFTWAREASP A:360 , ASP A:362 , ASP A:364 , TYR A:366 , ASP A:368 , HOH A:634binding site for residue CA A 503
04AC4SOFTWAREASP A:424 , ASP A:426 , ASN A:428 , TYR A:430 , ASP A:432 , HOH A:635binding site for residue CA A 504
05AC5SOFTWARESER B:132 , GLU B:229 , HOH B:633 , HOH B:634 , HOH B:637 , ASP C:1526binding site for residue MG B 501
06AC6SOFTWARESER B:134 , ASP B:137 , ASP B:138 , ALA B:342 , HOH B:632 , HOH B:638binding 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 512 through NAG A 513 bound to ASN A 43
09AC9SOFTWAREASN A:141binding site for Mono-Saccharide NAG A 516 bound to ASN A 141
10AD1SOFTWAREASN A:256 , SER A:277 , HOH A:721 , HOH A:812 , HOH A:828 , HOH A:850 , HOH A:955binding site for Mono-Saccharide NAG A 511 bound to ASN A 256
11AD2SOFTWAREASN A:266 , SER A:268 , ASP A:269 , HOH A:708binding site for Poly-Saccharide residues NAG A 514 through NAG A 515 bound to ASN A 266
12AD3SOFTWAREARG A:220 , ALA A:222 , SER A:223 , TYR A:226 , TYR A:261 , SER A:272 , LEU A:273 , ASN A:275 , HOH A:732 , HOH A:743 , HOH A:853 , HOH A:861 , HOH A:868 , HOH A:869 , HOH A:912 , HOH A:930binding site for Poly-Saccharide residues NAG A 505 through MAN A 510 bound to ASN A 275
13AD4SOFTWARETRP B:247 , ASN B:249 , THR B:431binding site for Poly-Saccharide residues NAG B 504 through NAG B 505 bound to ASN B 249
14AD5SOFTWAREASN B:141 , ASN B:343 , SER B:345binding site for Mono-Saccharide NAG B 509 bound to ASN B 343
15AD6SOFTWAREGLY B:384 , ASN B:386binding site for Poly-Saccharide residues NAG B 506 through NAG B 507 bound to ASN B 386
16AD7SOFTWARELYS B:382 , ASN B:383 , ASN B:397binding site for Mono-Saccharide NAG B 508 bound to ASN B 397

(-) 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 4WK0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WK0)

(-) Exons   (0, 0)

(no "Exon" information available for 4WK0)

(-) 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:449
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..........eeee.......eeeeee..............eeeeee.....ee..........hhhhh.........ee.........eeee..eeeeee...ee............eeeeee....eeeee....................eeee.....eeeee.hhhhhh.eeeeehhhhhhhh.............ee....hhhhh.......eeee........eeeeee........eeeee......eeeeee...........eeee........eeeeee...eee.....eee..eeeee.ee..ee.....eeee...........eeeee........eeeeee.........eeeee............eee...............eeeeee........eeeeeehhh.eeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4wk0 A    1 FNLDAEAPAVLSGPPGSFFGFSVEFYRPGTDGVSVLVGAPKANTSQPGVLQGGAVYLCPWGAQCTPIEFDSKGSRLLESSLSSSEGEEPVEYKSLQWFGATVRAHGSSILACAPLYSWRTEKEPLSDPVGTCYLSTDNFTRILEYAPCRSDFSWAAGQGYCQGGFSAEFTKTGRVVLGGPGSYFWQGQILSATQEQIAESYYPEYLINLVQGQLQTRQASSIYDDSYLGYSVAVGEFSGDDTEDFVAGVPKGNLTYGYVTILNGSDIRSLYNFSGEQMASYFGYAVAATDVNGDGLDDLLVGAPLLMDRTPDGRPQEVGRVYVYLQHPAGIEPTPTLTLTGHDEFGRFGSSLTPLGDLDQDGYNDVAIGAPFGGETQQGVVFVFPGGPGGLGSKPSQVLQPLWAASHTPDFFGSALRGGRDLDGNGYPDLIVGSFGVDKAVVYRGRPVV  452
                                    10        20        30        40        50        60 ||     73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443         
                                                                                        62|                                                                                                                                                                                                                                                                                                                                                                                                  
                                                                                         66                                                                                                                                                                                                                                                                                                                                                                                                  


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.......hhh.eeehhhhhh.............eeeeee.......hhhhh..ee..eeeeeee....eeeeeeee......eeeeeeee.hhhhhhhhhhh.hhhhhhhhhhh.....eeeeeeee...........hhhhhhh.............eeeeeeee.hhhhhhhhhh............hhhhhhhhhhhhhhhh.....eeeeeeee.......hhhhhhh..........ee..ee.........hhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhh.eeeee......eeeeeeee.hhh.eehhhhh.ee.......eeeeeeeeee........eeeeeee......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4wk0 B    5 NRCLKANAKSCGECIQAGPNCGWCTNSTFLTSARCDDLEALKKKGCPPDDIENPRGSKDIKKNKNVTNLKPEDITQIQPQQLVLRLRSGEPQTFTLKFKRAEDYPIDLYYLMDLSYSMKDDLENVKSLGTDLMNEMRRITSDFRIGFGSFVEKTVMPYISTTPAKLRNPCTSEQNCTTPFSYKNVLSLTNKGEVFNELVGKQRISGNLDSPEGGFDAIMQVAVCGSLIGWRNVTRLLVFSTDAGFHFAGDGKLGGIVLPNDGQCHLENNMYTMSHYYDYPSIAHLVQKLSENNIQTIFAVTEEFQPVYKELKNLIPKSAVGTLSANSSNVIQLIIDAYNSLSSEVILENGKLSEGVTISYKSYCKNGVNGTGENGRKCSNISIGDEVQFEISITSNKCPKKDSDSFKIRPLGFTEEVEVILQYICEC  444
                                    14        24        34|       49        59        69       |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|                                                                                                                                                                                                                                                                                                                                                                      
                                                         40                                    86                                                                                                                                                                                                                                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:3
                                    
               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
                4wk0 C 1524 RGD 1526
   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 4WK0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WK0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WK0)

(-) 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 | P08648: 3vi3 3vi4 4wjk 4wk2 4wk4
        ITB1_HUMAN | P05556: 1k11 1lha 3g9w 3t9k 3vi3 3vi4 4dx9 4wjk 4wk2 4wk4

(-) Related Entries Specified in the PDB File

4wjk 4wk2 4wk4