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(-) Description

Title :  RE-REFINEMENT OF THE CRYSTAL STRUCTURE OF THE PLEXIN-SEMAPHORIN-INTEGRIN DOMAIN/HYBRID DOMAIN/I-EGF1 SEGMENT FROM THE HUMAN INTEGRIN B2 SUBUNIT
 
Authors :  M. Sen, T. A. Springer
Date :  10 Oct 15  (Deposition) - 02 Mar 16  (Release) - 15 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
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 BETA-2
    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 23-125, 365-482
    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

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1FUL1Ligand/IonBETA-L-FUCOSE
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:28 , HIS A:438 , ASN A:458 , GLU A:460 , HOH A:695 , HOH A:753binding site for Poly-Saccharide residues NAG A 503 through FUL A 505 bound to ASN A 28
2AC2SOFTWAREALA A:92 , ASN A:94 , PHE A:363 , ARG A:371 , GLN A:390 , HOH A:612binding site for Poly-Saccharide residues NAG A 501 through NAG A 502 bound to ASN A 94

(-) SS Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:21
2A:11 -A:425
3A:14 -A:40
4A:24 -A:51
5A:364 -A:378
6A:398 -A:423
7A:427 -A:445
8A:437 -A:448
9A:450 -A:459

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:77 -Pro A:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E6V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E6V)

(-) Exons   (0, 0)

(no "Exon" information available for 5E6V)

(-) 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:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhh.....eee..........hhhh.eehhhhhhhh..hhh.ee....eeeee.........ee..eeeeee.....eeeeeee.....eeeeeeee......eeeeeeee.....eeeee..eeeeee.....eeeeeeeee......eeeeeee......eeeeeee.............hhhhh.eeee..eeee...ee.....ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e6v A   1 xECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDPTSLAETQEDHNGGQKQLSPQKVTLYLRPGQAAAFNVTFRRAKGYSRVFLDHNALPDTLKVTYDSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSFVIRALGFTDIVTVQVLPQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCEHHH 463
                            |       10        20        30        40        50        60        70        80        90       100  ||   349       359       369       379       389       399       409       419       429       439       449       459    
                            |                                                                                                   103|                                                                                                                        
                            1-PCA                                                                                                343
   Legend:   → Mismatch (orange background)
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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 5E6V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E6V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E6V)

(-) Gene Ontology  (46, 46)

Asymmetric/Biological Unit(hide GO term definitions)

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  5e6v
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  ITB2_HUMAN | P05107
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 Related Entries

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

UniProtKB/Swiss-Prot
        ITB2_HUMAN | P05107: 1jx3 1l3y 1yuk 2jf1 2p26 2p28 2v7d 3k6s 3k71 3k72 4neh 4nen 5e6r 5e6s 5e6u 5e6w 5e6x 5es4

(-) Related Entries Specified in the PDB File

1yuk THIS ENTRY 5E6V REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R1YUKSF