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(-) Description

Title :  COMPLEX OF 3'-SULFO-LEWIS-X WITH A SELECTIN-LIKE MUTANT OF MANNOSE-BINDING PROTEIN A
 
Authors :  K. K. -S. Ng, W. I. Weis
Date :  07 Nov 96  (Deposition) - 12 Feb 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  1,2,3
Keywords :  Lectin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. K. Ng, W. I. Weis
Structure Of A Selectin-Like Mutant Of Mannose-Binding Protein Complexed With Sialylated And Sulfated Lewis(X) Oligosaccharides.
Biochemistry V. 36 979 1997
PubMed-ID: 9033386  |  Reference-DOI: 10.1021/BI962564E
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MANNOSE-BINDING PROTEIN-A
    Chains: 1, 2, 3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PINIIIOMPA2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CLOSTRIPAIN FRAGMENT
    Mutation: YES
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: K3

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : 123

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 20)

Asymmetric/Biological Unit (6, 20)
No.NameCountTypeFull Name
1CA10Ligand/IonCALCIUM ION
2CL3Ligand/IonCHLORIDE ION
3FUC3Ligand/IonALPHA-L-FUCOSE
4MAG1Ligand/IonBETA-METHYL-N-ACETYL-D-GLUCOSAMINE
5NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SGA2Ligand/IonO3-SULFONYLGALACTOSE

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
0111UNKNOWNCA 1:1 , ASP 1:161 , GLU 1:165 , ASP 1:188 , GLU 1:193 , ASP 1:194 , HOH 2:337CA SITE 1, PROTOMER 1.
0211_01UNKNOWNCA 1:1 , ASP 1:161 , GLU 1:165 , ASP 1:188 , GLU 1:193 , ASP 1:194 , HOH 2:337CA SITE 1, PROTOMER 1.
0312UNKNOWNCA 2:1 , ASP 2:161 , GLU 2:165 , ASP 2:188 , GLU 2:193 , ASP 2:194 , HOH 2:259CA SITE 1, PROTOMER 2.
0412_02UNKNOWNCA 2:1 , ASP 2:161 , GLU 2:165 , ASP 2:188 , GLU 2:193 , ASP 2:194 , HOH 2:259CA SITE 1, PROTOMER 2.
0513UNKNOWNCA 3:1 , ASP 3:161 , GLU 3:165 , ASP 3:188 , GLU 3:193 , ASP 3:194 , HOH 1:314CA SITE 1, PROTOMER 3.
0613_03UNKNOWNCA 3:1 , ASP 3:161 , GLU 3:165 , ASP 3:188 , GLU 3:193 , ASP 3:194 , HOH 1:314CA SITE 1, PROTOMER 3.
0721UNKNOWNCA 1:2 , GLU 1:185 , ASN 1:187 , GLU 1:193 , ASN 1:205 , ASP 1:206 , HOH 2:335CA SITE 2, PROTOMER 1.
0821_04UNKNOWNCA 1:2 , GLU 1:185 , ASN 1:187 , GLU 1:193 , ASN 1:205 , ASP 1:206 , HOH 2:335CA SITE 2, PROTOMER 1.
0922UNKNOWNCA 2:2 , GLU 2:185 , ASN 2:187 , GLU 2:193 , ASN 2:205 , ASP 2:206 , HOH 2:266CA SITE 2, PROTOMER 2.
1022_05UNKNOWNCA 2:2 , GLU 2:185 , ASN 2:187 , GLU 2:193 , ASN 2:205 , ASP 2:206 , HOH 2:266CA SITE 2, PROTOMER 2.
1123UNKNOWNCA 3:2 , GLU 3:185 , ASN 3:187 , GLU 3:193 , ASN 3:205 , ASP 3:206 , HOH 1:306 , HOH 1:307CA SITE 2, PROTOMER 3.
1223_06UNKNOWNCA 3:2 , GLU 3:185 , ASN 3:187 , GLU 3:193 , ASN 3:205 , ASP 3:206 , HOH 1:306 , HOH 1:307CA SITE 2, PROTOMER 3.
1331UNKNOWNCA 1:3 , GLU 1:165 , ASP 1:194 , HOH 2:338 , HOH 2:344 , HOH 2:345CA SITE 3, PROTOMER 1.
1432UNKNOWNCA 2:3 , GLU 2:165 , ASP 2:194 , HOH 2:260CA SITE 3, PROTOMER 2.
1533UNKNOWNCA 3:3 , GLU 3:165 , ASP 3:194 , HOH 2:357CA SITE 3, PROTOMER 3.
16AC1SOFTWAREHIS 1:189 , GLU 1:193 , MAG 1:223 , FUC 1:224 , HOH 1:321 , HOH 1:326 , HOH 1:327 , HOH 1:329BINDING SITE FOR RESIDUE SGA 1 222
17AC5SOFTWAREHIS 3:189 , GLU 3:193 , NAG 3:223 , FUC 3:224 , HOH 3:337BINDING SITE FOR RESIDUE SGA 3 222
18AC6SOFTWAREHOH 1:230 , ASN 3:187 , HIS 3:189 , SGA 3:222 , FUC 3:224BINDING SITE FOR RESIDUE NAG 3 223
19AC7SOFTWARECA 3:2 , GLU 3:185 , ASN 3:187 , GLU 3:193 , ASN 3:205 , ASP 3:206 , SGA 3:222 , NAG 3:223BINDING SITE FOR RESIDUE FUC 3 224
20AC8SOFTWAREASP 1:161 , GLU 1:165 , ASP 1:188 , GLU 1:193 , ASP 1:194 , HOH 1:308BINDING SITE FOR RESIDUE CA 1 1
21AC9SOFTWAREGLU 1:185 , ASN 1:187 , GLU 1:193 , ASN 1:205 , ASP 1:206 , FUC 1:224BINDING SITE FOR RESIDUE CA 1 2
22BC1SOFTWAREGLU 1:84 , GLU 1:165 , ASP 1:194 , HOH 1:337 , HOH 1:338 , HOH 1:397BINDING SITE FOR RESIDUE CA 1 3
23BC2SOFTWAREHOH 1:282 , GLU 2:93 , HOH 2:311 , HOH 2:312 , HOH 2:313 , HOH 2:316BINDING SITE FOR RESIDUE CA 1 4
24BC6SOFTWAREGLU 2:165 , ASP 2:194 , HOH 2:364 , HOH 2:365BINDING SITE FOR RESIDUE CA 2 3
25BC7SOFTWAREASP 2:194 , SER 2:208 , CYS 2:209BINDING SITE FOR RESIDUE CL 2 4
26BC8SOFTWAREASP 3:161 , GLU 3:165 , ASP 3:188 , GLU 3:193 , ASP 3:194 , HOH 3:278BINDING SITE FOR RESIDUE CA 3 1
27BC9SOFTWAREGLU 3:185 , ASN 3:187 , GLU 3:193 , ASN 3:205 , ASP 3:206 , FUC 3:224BINDING SITE FOR RESIDUE CA 3 2
28CC1SOFTWAREGLU 3:84 , GLU 3:165 , ASP 3:194 , HOH 3:328 , HOH 3:330 , HOH 3:331BINDING SITE FOR RESIDUE CA 3 3
29CC2SOFTWAREASP 3:194 , CYS 3:209 , HOH 3:332BINDING SITE FOR RESIDUE CL 3 4

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
11:128 -1:217
21:195 -1:209
32:128 -2:217
42:195 -2:209
53:128 -3:217
63:195 -3:209

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Glu 1:185 -Pro 1:186
2Glu 2:185 -Pro 2:186
3Glu 3:185 -Pro 3:186

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 6)

Asymmetric/Biological Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.MBL1_RAT123-235
 
 		  31:106-218
2:106-218
3:106-218
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.MBL1_RAT212-234
 
 		  31:195-217
2:195-217
3:195-217

(-) Exons   (3, 9)

Asymmetric/Biological Unit (3, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000157231ENSRNOE00000411163chr16:17591820-1759188162MBL1_RAT-00--
1.2ENSRNOT000000157232ENSRNOE00000110617chr16:17593783-17593943161MBL1_RAT1-51510--
1.3ENSRNOT000000157233ENSRNOE00000110943chr16:17594301-17594417117MBL1_RAT51-904031:73-73
2:73-73
3:73-73		1
1
1
1.4ENSRNOT000000157234ENSRNOE00000111237chr16:17596168-1759624275MBL1_RAT90-1152631:73-98
2:73-98
3:73-98		26
26
26
1.5ENSRNOT000000157235ENSRNOE00000111555chr16:17597083-17597859777MBL1_RAT115-23812431:98-221
2:98-221
3:98-221		124
124
124

(-) 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:149
 aligned with MBL1_RAT | P19999 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:149
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229         
             MBL1_RAT    90 AIEVKLANMEAEINTLKSKLELTNKLHAFSMGKKSGKKFFVTNHERMPFSKVKALCSELRGTVAIPRNAEENKAIQEVAKTSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDEPNDHGSGEDCVTIVDNGLWNDISCQASHTAVCEFPA 238
               SCOP domains d3kmb12 1:73-104                d3kmb11 1:105-221 Mannose-binding protein A, C-lectin domain                                                          SCOP domains
               CATH domains 3kmb100 1:73-221 Mannose-Binding Protein A, subunit A                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeee...eeehhhhhhhhhhh.........hhhhhhhhhhh...........................................eeee.hhh.eeee....eee.eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------C_TYPE_LECTIN_2  PDB: 1:106-218 UniProt: 123-235                                                                 --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1        ---- PROSITE (2)
           Transcript 1 (1) 1------------------------Exon 1.5  PDB: 1:98-221 UniProt: 115-238                                                                                     Transcript 1 (1)
           Transcript 1 (2) Exon 1.4  PDB: 1:73-98    --------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3kmb 1  73 AIEVKLANMEAEINTLKSKLELTNKLHAFSMGKKSGKKFFVTNHERMPFSKVKALCSELRGTVAIPRNAEENKAIQEVAKTSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDEPNDHGSGEDCVTIVDNGLWNDISCQKKKTAVCEFPA 221
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212         


Chain 2 from PDB  Type:PROTEIN  Length:149
 aligned with MBL1_RAT | P19999 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:149
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229         
             MBL1_RAT    90 AIEVKLANMEAEINTLKSKLELTNKLHAFSMGKKSGKKFFVTNHERMPFSKVKALCSELRGTVAIPRNAEENKAIQEVAKTSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDEPNDHGSGEDCVTIVDNGLWNDISCQASHTAVCEFPA 238
               SCOP domains d3kmb22 2:73-104                d3kmb21 2:105-221 Mannose-binding protein A, C-lectin domain                                                          SCOP domains
               CATH domains 3kmb200 2:73-221 Mannose-Binding Protein A, subunit A                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee......hhhhhhhhhh..........hhhhhhhhhhh...........................................eeee.hhh.eeee........eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------C_TYPE_LECTIN_2  PDB: 2:106-218 UniProt: 123-235                                                                 --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1        ---- PROSITE (2)
           Transcript 1 (1) 1------------------------Exon 1.5  PDB: 2:98-221 UniProt: 115-238                                                                                     Transcript 1 (1)
           Transcript 1 (2) Exon 1.4  PDB: 2:73-98    --------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3kmb 2  73 AIEVKLANMEAEINTLKSKLELTNKLHAFSMGKKSGKKFFVTNHERMPFSKVKALCSELRGTVAIPRNAEENKAIQEVAKTSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDEPNDHGSGEDCVTIVDNGLWNDISCQKKKTAVCEFPA 221
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212         


Chain 3 from PDB  Type:PROTEIN  Length:149
 aligned with MBL1_RAT | P19999 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:149
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229         
             MBL1_RAT    90 AIEVKLANMEAEINTLKSKLELTNKLHAFSMGKKSGKKFFVTNHERMPFSKVKALCSELRGTVAIPRNAEENKAIQEVAKTSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDEPNDHGSGEDCVTIVDNGLWNDISCQASHTAVCEFPA 238
               SCOP domains d3kmb32 3:73-104                d3kmb31 3:105-221 Mannose-binding protein A, C-lectin domain                                                          SCOP domains
               CATH domains 3kmb300 3:73-221 Mannose-Binding Protein A, subunit A                                                                                                 CATH domains
           Pfam domains (1) --------------------------------------------Lectin_C-3kmb301 3:117-219                                                                             -- Pfam domains (1)
           Pfam domains (2) --------------------------------------------Lectin_C-3kmb302 3:117-219                                                                             -- Pfam domains (2)
           Pfam domains (3) --------------------------------------------Lectin_C-3kmb303 3:117-219                                                                             -- Pfam domains (3)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee......hhhhhhhhhh..........hhhhhhhhhhh...........................................eeee.....eeee........eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------C_TYPE_LECTIN_2  PDB: 3:106-218 UniProt: 123-235                                                                 --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1        ---- PROSITE (2)
           Transcript 1 (1) 1------------------------Exon 1.5  PDB: 3:98-221 UniProt: 115-238                                                                                     Transcript 1 (1)
           Transcript 1 (2) Exon 1.4  PDB: 3:73-98    --------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3kmb 3  73 AIEVKLANMEAEINTLKSKLELTNKLHAFSMGKKSGKKFFVTNHERMPFSKVKALCSELRGTVAIPRNAEENKAIQEVAKTSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDEPNDHGSGEDCVTIVDNGLWNDISCQKKKTAVCEFPA 221
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212
   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  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

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

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain 1,2,3   (MBL1_RAT | P19999)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0048306    calcium-dependent 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), in the presence of calcium.
    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: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:0030247    polysaccharide binding    Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    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).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
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:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    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:0051873    killing by host of symbiont cells    Any process mediated by an organism that results in the death of cells in the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction.
    GO:0044130    negative regulation of growth of symbiont in host    Any process in which the symbiont stops, prevents or reduces its increase in size or mass within the cells or tissues of the host organism. The host is defined as the larger of the organisms involved in the symbiotic interaction.
    GO:0050766    positive regulation of phagocytosis    Any process that activates or increases the frequency, rate or extent of phagocytosis.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0070207    protein homotrimerization    The formation of a protein homotrimer, a macromolecular structure consisting of three noncovalently associated identical subunits.
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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  MBL1_RAT | P19999
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        MBL1_RAT | P19999: 1afa 1afb 1afd 1bch 1bcj 1buu 1fif 1fih 1kmb 1kwt 1kwu 1kwv 1kww 1kwx 1kwy 1kwz 1kx0 1kx1 1msb 1rtm 1ytt 2kmb 2msb 4kmb

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