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(-) Description

Title :  COMPLEX OF MBP-C AND HIGH-AFFINITY LINEAR TRIMANNOSE
 
Authors :  K. K. Ng, A. R. Kolatkar, S. Park-Snyder, H. Feinberg, D. A. Clark, K. Drickamer, W. I. Weis
Date :  06 Feb 02  (Deposition) - 05 Jul 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  1,2
Keywords :  Protein-Carbohydrate Complex, Immune System, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. K. Ng, A. R. Kolatkar, S. Park-Snyder, H. Feinberg, D. A. Clark, K. Drickamer, W. I. Weis
Orientation Of Bound Ligands In Mannose-Binding Proteins. Implications For Multivalent Ligand Recognition.
J. Biol. Chem. V. 277 16088 2002
PubMed-ID: 11850428  |  Reference-DOI: 10.1074/JBC.M200493200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MANNOSE-BINDING PROTEIN C
    Chains1, 2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPINOMPIIIA2
    Expression System StrainJA221
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSUBTILISIN FRAGMENT (RESIDUES 129-243 OF P08661)
    GeneMBL1
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymMBP-C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit 12

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3MAN2Ligand/IonALPHA-D-MANNOSE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU 1:190 , ASN 1:192 , GLU 1:198 , ASN 1:210 , ASP 1:211 , CA 1:502 , HOH 1:1106 , HOH 1:1108BINDING SITE FOR RESIDUE MAN 1 1001
2AC2SOFTWAREGLU 2:190 , ASN 2:192 , GLU 2:198 , ASN 2:210 , ASP 2:211 , CA 2:602 , HOH 2:2132BINDING SITE FOR RESIDUE MAN 2 2001
3AC3SOFTWAREASP 1:166 , GLU 1:170 , ASN 1:193 , GLU 1:198 , ASN 1:199 , HOH 1:1047BINDING SITE FOR RESIDUE CA 1 501
4AC4SOFTWAREGLU 1:190 , ASN 1:192 , GLU 1:198 , ASN 1:210 , ASP 1:211 , MAN 1:1001BINDING SITE FOR RESIDUE CA 1 502
5AC5SOFTWAREASN 1:199 , PRO 1:213 , CYS 1:214 , HOH 1:1017BINDING SITE FOR RESIDUE CL 1 503
6AC6SOFTWAREASP 2:166 , GLU 2:170 , ASN 2:193 , GLU 2:198 , ASN 2:199 , HOH 2:2006BINDING SITE FOR RESIDUE CA 2 601
7AC7SOFTWAREGLU 2:190 , ASN 2:192 , GLU 2:198 , ASN 2:210 , ASP 2:211 , MAN 2:2001BINDING SITE FOR RESIDUE CA 2 602

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
11:133 -1:222
21:200 -1:214
32:133 -2:222
42:200 -2:214

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu 1:190 -Pro 1:191
2Glu 2:190 -Pro 2:191

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.MBL2_RAT134-241
 
  21:116-223
2:116-223
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.MBL2_RAT218-240
 
  21:200-222
2:200-222

(-) Exons   (0, 0)

(no "Exon" information available for 1KZC)

(-) 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 1 from PDB  Type:PROTEIN  Length:111
 aligned with MBL2_RAT | P08661 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:111
                                   142       152       162       172       182       192       202       212       222       232       242 
             MBL2_RAT   133 KYFMSSVRRMPLNRAKALCSELQGTVATPRNAEENRAIQNVAKDVAFLGITDQRTENVFEDLTGNRVRYTNWNEGEPNNVGSGENCVVLLTNGKWNDVPCSDSFLVVCEFS 243
               SCOP domains d1kzc1_ 1: Mannose-binding protein A, C-lectin domain                                                           SCOP domains
               CATH domains 1kzc100 1:115-225 Mannose-Binding Protein A, subunit A                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhh..ee....hhhhhhhhhhhh...eeeeee........ee........................eeee.....eeee......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -C_TYPE_LECTIN_2  PDB: 1:116-223 UniProt: 134-241                                                            -- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------C_TYPE_LECTIN_1        --- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 1kzc 1 115 KYFMSSVRRMPLNRAKALCSELQGTVATPRNAEENRAIQNVAKDVAFLGITDQRTENVFEDLTGNRVRYTNWNEGEPNNVGSGENCVVLLTNGKWNDVPCSDSFLVVCEFS 225
                                   124       134       144       154       164       174       184       194       204       214       224 

Chain 2 from PDB  Type:PROTEIN  Length:112
 aligned with MBL2_RAT | P08661 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:112
                                   141       151       161       171       181       191       201       211       221       231       241  
             MBL2_RAT   132 KKYFMSSVRRMPLNRAKALCSELQGTVATPRNAEENRAIQNVAKDVAFLGITDQRTENVFEDLTGNRVRYTNWNEGEPNNVGSGENCVVLLTNGKWNDVPCSDSFLVVCEFS 243
               SCOP domains d1kzc2_ 2: Mannose-binding protein A, C-lectin domain                                                            SCOP domains
               CATH domains 1kzc200 2:114-225 Mannose-Binding Protein A, subunit A                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhh..ee....hhhhhhhhhhhh...eeeeeeeeee..eeee........................eeee.....eeee......eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --C_TYPE_LECTIN_2  PDB: 2:116-223 UniProt: 134-241                                                            -- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------C_TYPE_LECTIN_1        --- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1kzc 2 114 KKYFMSSVRRMPLNRAKALCSELQGTVATPRNAEENRAIQNVAKDVAFLGITDQRTENVFEDLTGNRVRYTNWNEGEPNNVGSGENCVVLLTNGKWNDVPCSDSFLVVCEFS 225
                                   123       133       143       153       163       173       183       193       203       213       223  

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1KZC)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain 1,2   (MBL2_RAT | P08661)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0005534    galactose binding    Interacting selectively and non-covalently with the aldohexose galactose (galacto-hexose), a common constituent of many oligo- and polysaccharides.
    GO:0005537    mannose binding    Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
    GO:0070273    phosphatidylinositol-4-phosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' position.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    GO:0043621    protein self-association    Interacting selectively and non-covalently with a domain within the same polypeptide.
biological process
    GO:0006958    complement activation, classical pathway    Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
    GO:0001867    complement activation, lectin pathway    Any process involved in the activation of any of the steps of the lectin pathway of the complement cascade which allows for the direct killing of microbes and the regulation of other immune processes.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0045917    positive regulation of complement activation    Any process that activates or increases the frequency, rate or extent of complement activation.
    GO:0010954    positive regulation of protein processing    Any process that increases the rate, frequency or extent of protein maturation by peptide bond cleavage.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0070207    protein homotrimerization    The formation of a protein homotrimer, a macromolecular structure consisting of three noncovalently associated identical subunits.
    GO:0051259    protein oligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
cellular component
    GO:0005581    collagen trimer    A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.
    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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MBL2_RAT | P086611bv4 1kza 1kzb 1kzd 1kze 1rdi 1rdj 1rdk 1rdl 1rdm 1rdn 1rdo

(-) Related Entries Specified in the PDB File

1kza
1kzb
1kzd
1kze
1rdo MBP-C