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(-) Description

Title :  N-TERMINAL OF SIALOADHESIN IN COMPLEX WITH ME-A-9-N-BENZOYL-AMINO-9-DEOXY-NEU5AC (BENZ COMPOUND)
 
Authors :  N. R. Zaccai, K. Maenaka, T. Maenaka, P. R. Crocker, R. Brossmer, S. Kelm, E. Y. Jones
Date :  14 Feb 03  (Deposition) - 16 May 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Lectin/Immune System, Immune System, Immunoglobulin Superfamily, Carbohydrate Binding, Siglec, Inhibitor Design (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. R. Zaccai, K. Maenaka, T. Maenaka, P. R. Crocker, R. Brossmer, S. Kelm, E. Y. Jones
Structure-Guided Design Of Sialic Acid-Based Siglec Inhibitors And Crystallographic Analysis In Complex With Sialoadhesin
Structure V. 11 557 2003
PubMed-ID: 12737821  |  Reference-DOI: 10.1016/S0969-2126(03)00073-X

(-) Compounds

Molecule 1 - SIALOADHESIN
    Chains: A
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHO CELL
    Expression System Plasmid: PEE14
    Expression System Taxid: 10029
    Fragment: DOMAIN ONE, IG-LIKE V-TYPE DOMAIN, RESIDUES 20-138
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: BOUND TO ME-A-N-BENZOYL-AMINO-9-DEOXY- NEU5AC, COORDINATE SYSTEM ORIGX ORIGX MATRIX (M) ORIGX VECTOR (V)
    Other Details - Source: CHO CELL STABLE EXPRESSION WITH PEE14 PLASMID
    Synonym: SND1, SIALIC ACID BINDING IG-LIKE LECTIN-1, SIGLEC-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1BND1Ligand/IonME-A-N-BENZOYL-AMINO-9-DEOXY-NEU5AC
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:48 , LYS A:58 , LYS A:62 , ARG A:65 , LYS A:77 , HOH A:2070 , HOH A:2071BINDING SITE FOR RESIDUE SO4 A 202
2AC2SOFTWARETRP A:2 , SER A:5 , CYS A:22 , ILE A:23 , SER A:25 , TYR A:44 , ARG A:97 , SER A:103 , ARG A:105 , TRP A:106 , LEU A:107 , VAL A:109 , HOH A:2006 , HOH A:2068 , HOH A:2069BINDING SITE FOR RESIDUE BND A 201

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:79

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OD9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OD9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OD9)

(-) Exons   (0, 0)

(no "Exon" information available for 1OD9)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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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:119
 aligned with SN_MOUSE | Q62230 from UniProtKB/Swiss-Prot  Length:1695

    Alignment length:119
                                    29        39        49        59        69        79        89        99       109       119       129         
             SN_MOUSE    20 TWGVSSPKNVQGLSGSCLLIPCIFSYPADVPVSNGITAIWYYDYSGKRQVVIHSGDPKLVDKRFRGRAELMGNMDHKVCNLLLKDLKPEDSGTYNFRFEISDSNRWLDVKGTTVTVTTD 138
               SCOP domains d1od9a_ A: N-terminal domain of sialoadhesin                                                                            SCOP domains
               CATH domains 1od9A00 A:1-119 Immunoglobulins                                                                                         CATH domains
               Pfam domains V-set-1od9A01 A:1-116                                                                                               --- Pfam domains
         Sec.struct. author ..eee...eeeee....eee..eee...........eeeeee......eeeee..hhhhhhhhhh..eee..hhhhh...eee...hhhhheeeeeeee.....eee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1od9 A   1 TWGVSSPKNVQGLSGSCLLIPCIFSYPADVPVSNGITAIWYYDYSGKRQVVIHSGDPKLVDKRFRGRAELMGNMDHKVCNLLLKDLKPEDSGTYNFRFEISDSNRWLDVKGTTVTVTTD 119
                                    10        20        30        40        50        60        70        80        90       100       110
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Ig (577)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SN_MOUSE | Q62230)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0070234    positive regulation of T cell apoptotic process    Any process that activates or increases the frequency, rate or extent of T cell death by apoptotic process.
    GO:2001238    positive regulation of extrinsic apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SN_MOUSE | Q62230: 1od7 1oda 1qfo 1qfp 1url 2bve

(-) Related Entries Specified in the PDB File

1od7 N-TERMINAL OF SIALOADHESIN IN COMPLEX WITH ME-A-9-N-(NAPHTHYL-2-CARBONYL)-AMINO-9- DEOXY-NEU5AC (NAP COMPOUND)
1oda N-TERMINAL OF SIALOADHESIN IN COMPLEX WITH ME-A-9-N-((BIPHENYL-4-CARBONYL)-AMINO-9- DEOXY-NEU5AC (BIP COMPOUND)
1qfo N-TERMINAL DOMAIN OF SIALOADHESIN (MOUSE) IN COMPLEX WITH 3'SIALYLLACTOSE
1qfp N-TERMINAL DOMAIN OF SIALOADHESIN (MOUSE)