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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 :  T. A. Springer, M. Sen
Date :  10 Oct 15  (Deposition) - 02 Mar 16  (Release) - 15 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Cd18 Fragment, 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 Taxid: 9606
    Fragment: UNP RESIDUES 23-122, 362-574
    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  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:28binding site for Mono-Saccharide NAG A 902 bound to ASN A 28
2AC2SOFTWAREASN A:94 , LEU A:352 , GLN A:390 , HOH A:1001 , HOH A:1014 , HOH A:1020binding site for Mono-Saccharide NAG A 901 bound to ASN A 94

(-) SS Bonds  (17, 17)

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
10A:461 -A:492
11A:475 -A:490
12A:484 -A:495
13A:497 -A:512
14A:514 -A:537
15A:519 -A:535
16A:527 -A:540
17A:542 -A:551

(-) 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 5E6W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E6W)

(-) Exons   (0, 0)

(no "Exon" information available for 5E6W)

(-) 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:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhh...eee.hhhhh....hhhh.eehhhhhhhh..hhh.ee....eeeee.....ee..eeeeee.....eeeeeee.....eeeeeeee......eeeeeeee.....eeeee..eeeeee.....eeeeeeeee......eeeeeee.....eeeeeeee.................eeee..eeee...ee.....ee........hhhhh.....hhhhh.eeee..eeee.......................ee..ee......eeee..eeee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e6w A   1 QECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDPTSLAETQEDQKQLSPQKVTLYLRPGQAAAFNVTFRRAKLSSRVFLDHNALPDTLKVTYDSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSFVIRALGFTDIVTVQVLPQCECRCRDQSRSLCHGKGFLECGICRCDTGYIGKNCECQTQGRSQELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCECDTINCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQHHHH 556
                                    10        20        30        40        50        60       |74        84        94       104  ||   353       363       373       383       393       403       413       423       435       445       455       465||     476       486       496       506       516       526       536       546       556
                                                                                              68|                               107|                                                                                  432|                            466|                                                                                        
                                                                                               73                                347                                                                                   435                             468
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  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 5E6W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E6W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E6W)

(-) Gene Ontology  (46, 46)

Asymmetric/Biological Unit(hide GO term definitions)

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  5e6w
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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 5e6v 5e6x 5es4

(-) Related Entries Specified in the PDB File

2p28 THIS ENTRY 5E6W REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R2P28SF