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(-) Description

Title :  STRUCTURE OF A CHONDROITIN SULPHATE BINDING DBL3X FROM A VAR2CSA ENCODED PFEMP1 PROTEIN
 
Authors :  M. K. Higgins
Date :  20 Dec 07  (Deposition) - 24 Jun 08  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Malaria, Pregnancy, Pfemp1, Var2Csa, Dbl3X, Chondroitin Sulphate, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. K. Higgins
The Structure Of A Chondroitin Sulfate-Binding Domain Important In Placental Malaria.
J. Biol. Chem. V. 283 21842 2008
PubMed-ID: 18550531  |  Reference-DOI: 10.1074/JBC.C800086200

(-) Compounds

Molecule 1 - ERYTHROCYTE MEMBRANE PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: ORIGAMI B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DBL3X DOMAIN
    Gene: VAR
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833
    Strain: A4
    Synonym: PFEMP1 PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:1345 , GLN A:1348 , ILE A:1352 , PRO A:1442 , THR A:1443 , SER A:1452 , LYS A:1455 , HOH A:1586 , HOH A:1640BINDING SITE FOR RESIDUE GOL A 1

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:1219 -A:1418
2A:1230 -A:1273
3A:1251 -A:1264
4A:1344 -A:1437
5A:1462 -A:1546
6A:1476 -A:1501
7A:1486 -A:1576
8A:1505 -A:1574

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe A:1240 -Pro A:1241
2Asp A:1335 -Pro A:1336
3Pro A:1442 -Thr A:1443

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BQI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BQI)

(-) Exons   (0, 0)

(no "Exon" information available for 3BQI)

(-) 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:328
 aligned with Q6UDW7_PLAFA | Q6UDW7 from UniProtKB/TrEMBL  Length:3064

    Alignment length:360
                                  1227      1237      1247      1257      1267      1277      1287      1297      1307      1317      1327      1337      1347      1357      1367      1377      1387      1397      1407      1417      1427      1437      1447      1457      1467      1477      1487      1497      1507      1517      1527      1537      1547      1557      1567      1577
        Q6UDW7_PLAFA   1218 SCDLNATNYIRGCQSKTYDGKIFPGKGGEKQWICKDTIIHGDTNGACIPPRTQNLCVGELWDKSYGGRSNIKNDTKELLKEKIKNAIHKETELLYEYHDTGTAIISKNDKKGQKGKNDPNGLPKGFCHAVQRSFIDYKNMILGTSVNIYEHIGKLQEDIKKIIEKGTPQQKDKIGGVGSSTENVNAWWKGIEREMWDAVRCAITKINKKNNNSIFNGDECGVSPPTGNDEDQSVSWFKEWGEQFCIERLRYEQNIREACTINGKNEKKCINSKSGQGDKIQGACKRKCEKYKKYISEKKQEWDKQKTKYENKYVGKSASDLLKENYPECISANFDFIFNDNIEYKTYYPYGDYSSICSCE 1577
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................................eeeeeeee..eeeeee..hhhhh.hhh.ee.....ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh---------........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh....---------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................----hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-----...ee..-----.eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..hhhhhh...hhhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3bqi A 1218 SCDLNATNYIRGCQSKTYDGKIFPGKGGEKQWICKDTIIHGDTNGACIPPRTQNLCVGELWDKSYGGRSNIKNDTKELLKEKIKNAIHKETELLYEYHDTGTAIISK---------NDPNGLPKGFCHAVQRSFIDYKNMILGTSVNIYEHIGKLQEDIKKIIEKGTPQQ---------STENVNAWWKGIEREMWDAVRCAITKINKKNNNSIFNGDECGVSPPT----DQSVSWFKEWGEQFCIERLRYEQNIREACT-----EKKCINS-----DKIQGACKRKCEKYKKYISEKKQEWDKQKTKYENKYVGKSASDLLKENYPECISANFDFIFNDNIEYKTYYPYGDYSSICSCE 1577
                                  1227      1237      1247      1257      1267      1277      1287      1297      1307      1317      |  -      1337      1347      1357      1367      1377      1387      1397      1407      1417      1427      1437     |   -|     1457      1467      1477     |1487 |    1497      1507      1517      1527      1537      1547      1557      1567      1577
                                                                                                                                   1324      1334                                                 1387      1397                                          1443 1448                         1477  1483  1489  1495
   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 3BQI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3BQI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BQI)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q6UDW7_PLAFA | Q6UDW7)
molecular function
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q6UDW7_PLAFA | Q6UDW7: 2y8d 3bqk 3bql 3cml 3cpz 4p1t

(-) Related Entries Specified in the PDB File

3bqk 3bql