Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  MANNOSE-BINDING PROTEIN, SUBTILISIN DIGEST FRAGMENT COMPLEX WITH ALPHA-METHYL-D-MANNOPYRANOSIDE (0.2 M)
 
Authors :  K. K. -S. Ng, K. Drickamer, W. I. Weis
Date :  05 Sep 95  (Deposition) - 08 Mar 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  1,2
Keywords :  C-Type Lectin, Calcium-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. K. Ng, K. Drickamer, W. I. Weis
Structural Analysis Of Monosaccharide Recognition By Rat Liver Mannose-Binding Protein.
J. Biol. Chem. V. 271 663 1996
PubMed-ID: 8557671  |  Reference-DOI: 10.1074/JBC.271.2.663
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MANNOSE-BINDING PROTEIN-C
    Chains: 1, 2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PINIIIOMPA2
    Expression System Taxid: 562
    Fragment: SUBTILISIN FRAGMENT (RESIDUES 114 - 226)
    Organ: LIVER
    Organism Common: BLACK RAT
    Organism Scientific: RATTUS RATTUS
    Organism Taxid: 10117
    Other Details: THE BACTERIALLY EXPRESSED MATERIAL IS DIGESTED WITH SUBTILISIN TO PRODUCE THE PROTEIN USED IN THE CRYSTAL STRUCTURE ANALYSIS
    Synonym: SUB-MBP-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
3MMA2Ligand/IonO1-METHYL-MANNOSE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECA 1:2 , GLU 1:190 , ASN 1:192 , GLU 1:198 , ASN 1:210 , ASP 1:211 , HOH 1:343 , HOH 1:358 , HOH 1:360 , HOH 1:361BINDING SITE FOR RESIDUE MMA 1 1
02AC2SOFTWARECA 2:2 , GLU 2:190 , ASN 2:192 , GLU 2:198 , ASN 2:210 , ASP 2:211 , HOH 2:362 , HOH 2:367 , HOH 2:386BINDING SITE FOR RESIDUE MMA 2 1
03AC3SOFTWAREASP 1:166 , GLU 1:170 , ASN 1:193 , GLU 1:198 , ASN 1:199 , HOH 1:274BINDING SITE FOR RESIDUE CA 1 227
04AC4SOFTWAREMMA 1:1 , GLU 1:190 , ASN 1:192 , GLU 1:198 , ASN 1:210 , ASP 1:211BINDING SITE FOR RESIDUE CA 1 2
05AC5SOFTWAREASN 1:199 , PRO 1:213 , CYS 1:214 , HOH 1:243BINDING SITE FOR RESIDUE CL 1 3
06AC6SOFTWAREASP 2:166 , GLU 2:170 , ASN 2:193 , GLU 2:198 , ASN 2:199 , HOH 2:232BINDING SITE FOR RESIDUE CA 2 227
07AC7SOFTWAREMMA 2:1 , GLU 2:190 , ASN 2:192 , GLU 2:198 , ASN 2:210 , ASP 2:211BINDING SITE FOR RESIDUE CA 2 2
08CA1AUTHORCA 1:227 , ASP 1:166 , GLU 1:170 , ASN 1:193 , GLU 1:198 , ASN 1:199 , HOH 1:274CALCIUM BINDING SITES
09CA2AUTHORCA 2:227 , ASP 2:166 , GLU 2:170 , ASN 2:193 , GLU 2:198 , ASN 2:199 , HOH 2:232CALCIUM BINDING SITES
10CA3AUTHORCA 1:2 , GLU 1:190 , ASN 1:192 , GLU 1:198 , ASN 1:210 , ASP 1:211 , MMA 1:1CALCIUM BINDING SITES
11CA4AUTHORCA 2:2 , GLU 2:190 , ASN 2:192 , GLU 2:198 , ASN 2:210 , ASP 2:211 , MMA 2:1CALCIUM BINDING SITES

(-) 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 1RDL)

(-) 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 1RDL)

(-) 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 d1rdl1_ 1: Mannose-binding protein A, C-lectin domain                                                           SCOP domains
               CATH domains 1rdl100 1:115-225 Mannose-Binding Protein A, subunit A                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhh.........hhhhhhhhhh............................................eeee.....eeee........eeee. 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
                 1rdl 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 d1rdl2_ 2: Mannose-binding protein A, C-lectin domain                                                            SCOP domains
               CATH domains 1rdl200 2:114-225 Mannose-Binding Protein A, subunit A                                                           CATH domains
           Pfam domains (1) --------Lectin_C-1rdl201 2:122-224                                                                             - Pfam domains (1)
           Pfam domains (2) --------Lectin_C-1rdl202 2:122-224                                                                             - Pfam domains (2)
         Sec.struct. author ..eeee......hhhhhhhhhhh.........hhhhhhhhhh....eeeeee..................................eeee.....eeee........eeee. 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
                 1rdl 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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: C_Lectin (98)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    CA1  [ RasMol ]  +environment [ RasMol ]
    CA2  [ RasMol ]  +environment [ RasMol ]
    CA3  [ RasMol ]  +environment [ RasMol ]
    CA4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu 1:190 - Pro 1:191   [ RasMol ]  
    Glu 2:190 - Pro 2:191   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1rdl
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MBL2_RAT | P08661
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MBL2_RAT | P08661
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MBL2_RAT | P08661: 1bv4 1kza 1kzb 1kzc 1kzd 1kze 1rdi 1rdj 1rdk 1rdm 1rdn 1rdo

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1RDL)