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(-) Description

Title :  HIGH RESOLUTION STRUCTURE OF MANNOSE BINDING LECTIN FROM CHAMPEDAK (CMB)
 
Authors :  M. Gabrielsen, P. S. Abdul-Rahman, S. Othman, O. H. Hashim, R. J. Cogdel
Date :  22 Feb 12  (Deposition) - 27 Feb 13  (Release) - 18 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Gabrielsen, P. S. Abdul-Rahman, S. Othman, O. H. Hashim, R. J. Cogdell
Structures And Binding Specificity Of Galactose- And Mannose-Binding Lectins From Champedak: Differences From Jackfruit Lectins
Acta Crystallogr. , Sect. F V. 70 709 2014
PubMed-ID: 24915077  |  Reference-DOI: 10.1107/S2053230X14008966
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MANNOSE-SPECIFIC LECTIN KM+
    Chains: A, B, C, D
    Organism Scientific: ARTOCARPUS INTEGER
    Organism Taxid: 3490
    Synonym: CHAMPEDAK MANNOSE BINDING LECTIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
1CD8Ligand/IonCADMIUM ION
2CL7Ligand/IonCHLORIDE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:69 , HOH A:2043BINDING SITE FOR RESIDUE CD A1151
02AC2SOFTWAREASP B:115 , CD B:1153 , CL B:1154 , CL B:1155 , CL B:1156 , ASP D:115BINDING SITE FOR RESIDUE CD B1151
03AC3SOFTWAREASP B:115 , CL B:1154 , CL B:1155 , CL B:1157BINDING SITE FOR RESIDUE CD B1152
04AC4SOFTWARECD B:1151 , CL B:1156 , ASP D:115BINDING SITE FOR RESIDUE CD B1153
05AC5SOFTWARECD B:1151 , CD B:1152 , GLU D:117BINDING SITE FOR RESIDUE CL B1154
06AC6SOFTWAREASP B:115 , CD B:1151 , CD B:1152 , PHE D:87 , ARG D:98 , ASP D:115BINDING SITE FOR RESIDUE CL B1155
07AC7SOFTWARESER B:88 , CD B:1151 , CD B:1153 , ASP D:115BINDING SITE FOR RESIDUE CL B1156
08AC8SOFTWARECD B:1152 , SER D:88 , ARG D:98BINDING SITE FOR RESIDUE CL B1157
09AC9SOFTWAREGLU A:117 , CD C:1152 , CL C:1154 , CL C:1155BINDING SITE FOR RESIDUE CD C1151
10BC1SOFTWARESER A:88 , GLU A:117 , ASP C:115 , CD C:1151 , CL C:1153 , CL C:1154BINDING SITE FOR RESIDUE CD C1152
11BC2SOFTWARESER A:88 , CD C:1152BINDING SITE FOR RESIDUE CL C1153
12BC3SOFTWAREPHE A:87 , ARG A:98 , ASP C:115 , CD C:1151 , CD C:1152BINDING SITE FOR RESIDUE CL C1154
13BC4SOFTWAREASP A:115 , GLU A:117 , CD C:1151 , CD C:2000BINDING SITE FOR RESIDUE CL C1155
14BC5SOFTWAREASP A:115 , GLU A:117 , CL C:1155BINDING SITE FOR RESIDUE CD C2000
15BC6SOFTWAREGLU D:74 , HOH D:2047 , HOH D:2071 , HOH D:2072BINDING SITE FOR RESIDUE CD D1151

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AKD)

(-) Cis Peptide Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1Gly A:9 -Pro A:10
2Phe A:72 -Pro A:73
3Leu A:90 -Ala A:91
4Gly A:111 -Pro A:112
5Gly B:9 -Pro B:10
6Phe B:72 -Pro B:73
7Leu B:90 -Ala B:91
8Gly B:111 -Pro B:112
9Met C:1 -Ala C:2
10Gly C:9 -Pro C:10
11Gly C:15 -Gly C:16
12Phe C:72 -Pro C:73
13Gly C:111 -Pro C:112
14Gly D:9 -Pro D:10
15Phe D:72 -Pro D:73
16Gly D:111 -Pro D:112

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AKD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AKD)

(-) Exons   (0, 0)

(no "Exon" information available for 4AKD)

(-) 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:150
 aligned with Q7M1T4_ARTIN | Q7M1T4 from UniProtKB/TrEMBL  Length:149

    Alignment length:150
                             1                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149
         Q7M1T4_ARTIN     - -ASQTITVGPWGGPGGNGWDDGSYTGIRQIELSYKEAIGSFSVIYDLNGEPFSGPKHTSKLPYKNVKIELRFPDEFLESVSGYTAPFSALATPTPVVRSLTFKTNKGRTFGPYGDEEGTYFNLPIENGLIVGFKGRTGDLLDAIGVHMAL 149
               SCOP domains d4akda_ A: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeee....eeee.....eeeeeeeee...eeeeeeeeee..eeeeeeee......eeeeee.......eeeeeeeee..........eeeeeeeee....eeeeee....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4akd A   1 MASQTITVGPWGGSGGNGWDDGSYTGIRQIELSYKEAIGSFCVIYDLNGESFPGPKHTSKLPYKNVKIELQFPEEFLVSVSGYTGPFSALATPTPVVRSLTFKTNKGRTFGPYGDEEGTYFNLPIENGLIVGFKGRTGDLLDAIGVHMAL 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150


Chain B from PDB  Type:PROTEIN  Length:150
 aligned with Q7M1T4_ARTIN | Q7M1T4 from UniProtKB/TrEMBL  Length:149

    Alignment length:150
                             1                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149
         Q7M1T4_ARTIN     - -ASQTITVGPWGGPGGNGWDDGSYTGIRQIELSYKEAIGSFSVIYDLNGEPFSGPKHTSKLPYKNVKIELRFPDEFLESVSGYTAPFSALATPTPVVRSLTFKTNKGRTFGPYGDEEGTYFNLPIENGLIVGFKGRTGDLLDAIGVHMAL 149
               SCOP domains d4akdb_ B: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeee....eeee.....eeeeeeeee...eeeeeeeeee..eeee..........eeeeee.......eeeeeeeee..........eeeeeeeee....eeeeee....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4akd B   1 MASQTITVGPWGGSGGNGWDDGSYTGIRQIELSYKEAIGSFCVIYDLNGESFPGPKHTSKLPYKNVKIELQFPEEFLVSVSGYTGPFSALATPTPVVRSLTFKTNKGRTFGPYGDEEGTYFNLPIENGLIVGFKGRTGDLLDAIGVHMAL 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150


Chain C from PDB  Type:PROTEIN  Length:144
 aligned with Q7M1T4_ARTIN | Q7M1T4 from UniProtKB/TrEMBL  Length:149

    Alignment length:150
                             1                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149
         Q7M1T4_ARTIN     - -ASQTITVGPWGGPGGNGWDDGSYTGIRQIELSYKEAIGSFSVIYDLNGEPFSGPKHTSKLPYKNVKIELRFPDEFLESVSGYTAPFSALATPTPVVRSLTFKTNKGRTFGPYGDEEGTYFNLPIENGLIVGFKGRTGDLLDAIGVHMAL 149
               SCOP domains d4akdc_ C: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeee....eeee.....eeeeeeeee...eeeeeeeeee..eeee..........eeeeee.......eeeeeee.------........eeeeee....eeeeee......eeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4akd C   1 MASQTITVGPWGGSGGNGWDDGSYTGIRQIELSYKEAIGSFCVIYDLNGESFPGPKHTSKLPYKNVKIELQFPEEFLVSVSGYT------ATPTPVVRSLTFKTNKGRTFGPYGDEEGTYFNLPIENGLIVGFKGRTGDLLDAIGVHMAL 150
                                    10        20        30        40        50        60        70        80   |     -|      100       110       120       130       140       150
                                                                                                              84     91                                                           


Chain D from PDB  Type:PROTEIN  Length:150
 aligned with Q7M1T4_ARTIN | Q7M1T4 from UniProtKB/TrEMBL  Length:149

    Alignment length:150
                             1                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149
         Q7M1T4_ARTIN     - -ASQTITVGPWGGPGGNGWDDGSYTGIRQIELSYKEAIGSFSVIYDLNGEPFSGPKHTSKLPYKNVKIELRFPDEFLESVSGYTAPFSALATPTPVVRSLTFKTNKGRTFGPYGDEEGTYFNLPIENGLIVGFKGRTGDLLDAIGVHMAL 149
               SCOP domains d4akdd_ D: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeee....eeee.....eeeeeeeee...eeeeeeeeee..eeee..........eeeeee.......eeeeeeeee..........eeeeeeeee....eeeeee....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4akd D   1 MASQTITVGPWGGSGGNGWDDGSYTGIRQIELSYKEAIGSFCVIYDLNGESFPGPKHTSKLPYKNVKIELQFPEEFLVSVSGYTGPFSALATPTPVVRSLTFKTNKGRTFGPYGDEEGTYFNLPIENGLIVGFKGRTGDLLDAIGVHMAL 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AKD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AKD)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4AKD)

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  Cis Peptide Bonds
    Gly A:111 - Pro A:112   [ RasMol ]  
    Gly A:9 - Pro A:10   [ RasMol ]  
    Gly B:111 - Pro B:112   [ RasMol ]  
    Gly B:9 - Pro B:10   [ RasMol ]  
    Gly C:111 - Pro C:112   [ RasMol ]  
    Gly C:15 - Gly C:16   [ RasMol ]  
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    Gly D:111 - Pro D:112   [ RasMol ]  
    Gly D:9 - Pro D:10   [ RasMol ]  
    Leu A:90 - Ala A:91   [ RasMol ]  
    Leu B:90 - Ala B:91   [ RasMol ]  
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    Phe A:72 - Pro A:73   [ RasMol ]  
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 Related Entries

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

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        Q7M1T4_ARTIN | Q7M1T4: 1j4s 1j4t 1j4u 1vbo 1vbp

(-) Related Entries Specified in the PDB File

4ak4 HIGH RESOLUTION STRUCTURE OF GALACTOSE BINDING LECTIN FROM CHAMPEDAK (CGB)
4akb STRUCTURE OF GALACTOSE BINDING LECTIN FROM CHAMPEDAK ( CGB) WITH GALACTOSE
4akc STRUCTURE OF GALACTOSE BINDING LECTIN FROM CHAMPEDAK ( CGB) WITH GAL(BETA)1,3-GALNAC