Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURES OF LEUKOCYTE INTEGRIN ALB2: THE AI DOMAIN, THE HEADPIECE, AND THE POCKET FOR THE INTERNAL LIGAND
 
Authors :  M. Sen, T. A. Springer
Date :  10 Oct 15  (Deposition) - 06 Apr 16  (Release) - 11 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lymphocyte Function-Associated Antigen-1, Lfa-1, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sen, T. A. Springer
Leukocyte Integrin Alpha L Beta 2 Headpiece Structures: The Alpha I Domain, The Pocket For The Internal Ligand, And Concerted Movements Of Its Loops.
Proc. Natl. Acad. Sci. Usa V. 113 2940 2016
PubMed-ID: 26936951  |  Reference-DOI: 10.1073/PNAS.1601379113

(-) Compounds

Molecule 1 - INTEGRIN ALPHA-L
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Atcc Number: CRL-3022
    Expression System Cell Line: HEK
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 26-770
    Gene: ITGAL, CD11A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CD11 ANTIGEN-LIKE FAMILY MEMBER A,LEUKOCYTE ADHESION GLYCOPROTEIN LFA-1 ALPHA CHAIN,LFA-1A,LEUKOCYTE FUNCTION-ASSOCIATED MOLECULE 1 ALPHA CHAIN
 
Molecule 2 - INTEGRIN BETA-2
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Atcc Number: CRL-3022
    Expression System Cell Line: HEK
    Expression System Organ: KIDNEY
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 23-482
    Gene: ITGB2, CD18, MFI7
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CELL SURFACE ADHESION GLYCOPROTEINS LFA-1/CR3/P150,95 SUBUNIT BETA,COMPLEMENT RECEPTOR C3 SUBUNIT BETA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3MG2Ligand/IonMAGNESIUM ION
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:139 , SER A:141 , ASP A:239 , CL A:2004 , HOH A:4066 , HOH A:4091binding site for residue MG A 2001
02AC2SOFTWAREASP A:443 , ASP A:445 , ASP A:447 , GLU A:449 , GLU A:451 , HOH A:4154binding site for residue CA A 2002
03AC3SOFTWAREASP A:505 , ASN A:507 , ASP A:509 , LEU A:511 , ASP A:513 , HOH A:4041binding site for residue CA A 2003
04AC4SOFTWARESER A:139 , SER A:141 , THR A:206 , MG A:2001 , HOH A:4027binding site for residue CL A 2004
05AC5SOFTWARESER B:114 , GLU B:212 , HOH B:4009 , HOH B:4043 , HOH B:4068 , HOH B:4077binding site for residue MG B 2001
06AC6SOFTWARESER B:116 , ASP B:119 , ASP B:120 , GLU B:325 , HOH B:4032 , HOH B:4203binding site for residue CA B 2002
07AC7SOFTWAREASP B:151 , ASN B:207 , ASP B:209 , PRO B:211 , GLU B:212binding site for residue CA B 2003
08AC8SOFTWAREASN A:64 , GLN A:117 , HOH A:4285binding site for Mono-Saccharide NAG A 2005 bound to ASN A 64
09AC9SOFTWAREALA B:92 , ASN B:94 , GLN B:390binding site for Mono-Saccharide NAG B 2004 bound to ASN B 94
10AD1SOFTWAREARG B:143 , ASN B:190binding site for Mono-Saccharide NAG B 2005 bound to ASN B 190

(-) SS Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1A:48 -A:55
2A:86 -A:104
3A:94 -A:125
4B:3 -B:21
5B:11 -B:425
6B:14 -B:40
7B:24 -B:51
8B:169 -B:176
9B:224 -B:264
10B:364 -B:378
11B:398 -B:423
12B:427 -B:445
13B:437 -B:448
14B:450 -B:459

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:280 -Pro A:281
2Glu A:368 -Pro A:369
3Ser B:77 -Pro B:78
4Leu B:155 -Pro B:156

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E6U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E6U)

(-) Exons   (0, 0)

(no "Exon" information available for 5E6U)

(-) 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:583
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhheee............eeee..eeeeee........eeeeee.....eee...............eeee......eeeeeeeeeeee..eeeeeeeeeee.......eeee...........eeeeeeee.....hhhhhhhhhhhhhhhhhhh....eeeeeeee...eeeeehhhhhhh..hhhhhh..........hhhhhhhhhhhhh.hhhhh.....eeeeeeee.........hhhhh..eeeeeee.hhhhhhhhhhhhhhhh..hhhhheeee.hhhhhhhhhhhhhhh.............eeeeeeee..eeeeee.hhhhhh.eeeee......eeeee...............eeeee.......eeeeee.hhhhh.eeeeee........eeeeeee...........eeee.........eeeeee..........eeeeeee....eeeeee..............eeee...........eeeee......eeeee.ee..ee.....eeeehhhhh.........eeeee.......eeeeeee..eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e6u A   1 YNLDVRGARSFSPPRAGRHFGYRVLQVGNGVIVGAPGEGNSTGSLYQCQSGTGHCLPVTLRGSNYTSKYLGMTLATDPTDGSILACDPGLSRTCDQNTYLSGLCYLFRQNLQGPMLQGRPGFQECIKGNVDLVFLFDGSMSLQPDEFQKILDFMKDVMKKLSNTSYQFAAVQFSTSYKTEFDFSDYVKWKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGARPDATKVLIIITDGEATDSGNIDAAKDIIRYIIGIGKHFQTKESQETLHKFASKPASEFVKILDTFEKLKDLFTELQKKIQDLTSFNMELSSSGISADLSRGHAVVGAVGAKDWAGGFLDLKADLQDDTFIGNEPLTPEVRAGYLGYTVTWLPSRQKTSLLASGAPRYQHMGRVLLFQEPQGGGHWSQVQTIHGTQIGSYFGGELCGVDVDQDGETELLLIGAPLFYGEQRGGRVFIYQRRQLGFEEVSELQGDPGYPLGRFGEAITALTDINGDGLVDVAVGAPLEEQGAVYIFNGRHGGLSPQPSQRIEGTQVLSGIQWFGRSIHGVKDLEGDGLADVAVGAESQMIVLSSRPVV 591
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300     ||318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588   
                                                                                                                                                                                                                                                                                                                                           306|                                                                                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                                                                                                            315                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:453
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhh...eee...............eehhhhhhhh......ee....eeeee...ee..eeeeee.....eeeeeee.......eeeeeeee.hhhhhhhhhhhh.hhhhhhhhhhhhh...eeeeeee...........hhhhhhh..............eeeeeeee.hhhhhhhhhhh...........hhhhhhhhhhhhhhhhh....eeeeeeee.......hhhhhhh..........ee..ee.hhhh....hhhhhhhhhhhh.eeeeeee...hhhhhhhhhh.....eeee......hhhhhhhhhhhhhhh.eeeee......eeeeeeee.....eeeee..eee........eeeeeeeee......eeeeeee.....eeeeeeee....................eee..eee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e6u B   1 QECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDPTSLAETQQKQLSPQKVTLYLRPGQAAAFNVTFRRAKGYPIDLYYLMDLSYSMLDDLRNVKKLGGDLLRALNEITESGRIGFGSFVDKTVLPFVNTHPDKLRNPCPNKEKECQPPFAFRHVLKLTNNSNQFQTEVGKQLISGNLDAPEGGLDAMMQVAACPEEIGWRKVTRLLVFATDDGFHFAGDGKLGAILTPNDGRCHLEDNLYKRSNEFDYPSVGQLAHKLAENNIQPIFAVTSRMVKTYEKLTEIIPKSAVGELSEDSSNVVQLIKNAYNKLSSRVFLDHNALPDTLKVTYDSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSFVIRALGFTDIVTVQVLPQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNC 459
                                    10        20        30        40        50        60     || 76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456   
                                                                                            66|                                                                                                                                                                                                                                                                                                                                                                                                  
                                                                                             73
   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 5E6U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E6U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E6U)

(-) Gene Ontology  (50, 73)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:368 - Pro A:369   [ RasMol ]  
    Leu B:155 - Pro B:156   [ RasMol ]  
    Lys A:280 - Pro A:281   [ RasMol ]  
    Ser B:77 - Pro B:78   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5e6u
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ITAL_HUMAN | P20701
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  ITB2_HUMAN | P05107
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ITAL_HUMAN | P20701
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  ITB2_HUMAN | P05107
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ITAL_HUMAN | P20701: 1cqp 1dgq 1ij4 1lfa 1mjn 1mq8 1mq9 1mqa 1rd4 1t0p 1xdd 1xdg 1xuo 1zon 1zoo 1zop 2ica 2k8o 2m3e 2o7n 3bn3 3bqm 3bqn 3e2m 3eoa 3eob 3f74 3f78 3hi6 3m6f 3tcx 4ixd 5e6r 5e6s
        ITB2_HUMAN | P05107: 1jx3 1l3y 1yuk 2jf1 2p26 2p28 2v7d 3k6s 3k71 3k72 4neh 4nen 5e6r 5e6s 5e6v 5e6w 5e6x 5es4

(-) Related Entries Specified in the PDB File

5e6r 5e6s 5e6w 5e6x