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(-) Description

Title :  CRYSTAL STRUCTURE OF CEL-IV COMPLEXED WITH RAFFINOSE
 
Authors :  T. Hatakeyama, T. Hozawa, K. Ishii, T. Kamiya, S. Goda, M. Kusunoki, H. U
Date :  07 Aug 10  (Deposition) - 19 Jan 11  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Cel-Iv, C-Type Lectin, Raffinose, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hatakeyama, T. Kamiya, M. Kusunoki, S. Nakamura-Tsuruta, J. Hirabayashi, S. Goda, H. Unno
Galactose Recognition By A Tetrameric C-Type Lectin, Cel-Iv Containing The Epn Carbohydrate Recognition Motif
J. Biol. Chem. V. 286 10305 2011
PubMed-ID: 21247895  |  Reference-DOI: 10.1074/JBC.M110.200576

(-) Compounds

Molecule 1 - LECTIN CEL-IV, C-TYPE
    Chains: A, B, C, D
    Organism Common: SEA CUCUMBER
    Organism Scientific: CUCUMARIA ECHINATA
    Organism Taxid: 40245

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric/Biological Unit (3, 17)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2EDO9Ligand/Ion1,2-ETHANEDIOL
3RAF4Ligand/IonRAFFINOSE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:113 , ASN A:115 , ASN A:116 , ASP A:136 , RAF A:158BINDING SITE FOR RESIDUE CA A 201
02AC2SOFTWARETRP A:79 , GLN A:82 , GLU A:113 , ASN A:115 , ASN A:116 , TYR A:129 , ASP A:136 , VAL A:137 , EDO A:159 , CA A:201 , HOH A:572 , HOH A:604 , HOH A:624BINDING SITE FOR RESIDUE RAF A 158
03AC3SOFTWAREASN A:116 , VAL A:137 , TYR A:138 , ASN A:141 , RAF A:158 , HOH A:423BINDING SITE FOR RESIDUE EDO A 159
04AC4SOFTWAREALA A:80 , PRO A:81 , GLN A:82 , PHE A:143 , HOH A:382BINDING SITE FOR RESIDUE EDO A 160
05AC5SOFTWAREGLU B:113 , ASN B:115 , ASN B:116 , ASP B:136 , RAF B:158BINDING SITE FOR RESIDUE CA B 201
06AC6SOFTWARETRP B:79 , GLN B:82 , GLU B:113 , ASN B:115 , ASN B:116 , TYR B:129 , ALA B:135 , ASP B:136 , VAL B:137 , HOH B:173 , CA B:201 , HOH B:224 , HOH B:312 , HOH B:342 , HOH B:449 , HOH B:451 , HOH B:576 , HOH B:593 , ASN C:115 , GLY C:117 , TYR C:138 , EDO C:162 , HOH C:170 , HOH C:212BINDING SITE FOR RESIDUE RAF B 158
07AC7SOFTWARETYR B:138 , ASN B:141 , ASN C:116 , VAL C:137 , TYR C:138 , ASN C:141 , RAF C:158 , EDO C:161 , EDO C:162BINDING SITE FOR RESIDUE EDO B 159
08AC8SOFTWAREGLU C:113 , ASN C:115 , ASN C:116 , ASP C:136 , RAF C:158BINDING SITE FOR RESIDUE CA C 201
09AC9SOFTWAREASN B:115 , ASN B:116 , GLY B:117 , PRO B:118 , TYR B:138 , EDO B:159 , HOH B:463 , TRP C:79 , GLN C:82 , GLU C:113 , ASN C:115 , ASN C:116 , TYR C:129 , ASP C:136 , VAL C:137 , EDO C:161 , EDO C:162 , CA C:201 , HOH C:291BINDING SITE FOR RESIDUE RAF C 158
10BC1SOFTWARECYS A:41 , HIS C:55 , SER C:102 , SER C:103BINDING SITE FOR RESIDUE EDO C 159
11BC2SOFTWARESER C:70 , LEU C:71 , PRO C:72 , ASP C:73 , HOH D:329BINDING SITE FOR RESIDUE EDO C 160
12BC3SOFTWARETYR B:138 , ASN B:140 , ASN B:141 , EDO B:159 , GLN C:82 , VAL C:137 , ASN C:141 , RAF C:158BINDING SITE FOR RESIDUE EDO C 161
13BC4SOFTWAREASN B:116 , VAL B:137 , TYR B:138 , ASN B:141 , RAF B:158 , EDO B:159 , ASN C:116 , RAF C:158BINDING SITE FOR RESIDUE EDO C 162
14BC5SOFTWAREGLU D:113 , ASN D:115 , ASN D:116 , ASP D:136 , RAF D:158BINDING SITE FOR RESIDUE CA D 201
15BC6SOFTWARETRP D:79 , GLN D:82 , GLU D:113 , ASN D:115 , ASN D:116 , ASP D:136 , VAL D:137 , EDO D:159 , CA D:201 , HOH D:202 , HOH D:371BINDING SITE FOR RESIDUE RAF D 158
16BC7SOFTWAREASN D:116 , ASP D:136 , VAL D:137 , TYR D:138 , ASN D:141 , RAF D:158 , HOH D:230 , HOH D:473BINDING SITE FOR RESIDUE EDO D 159
17BC8SOFTWAREALA D:80 , PRO D:81 , GLN D:82 , PHE D:143 , HOH D:188 , HOH D:271BINDING SITE FOR RESIDUE EDO D 160

(-) SS Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1A:1 -D:1
2A:5 -A:16
3A:33 -A:147
4A:41 -C:151
5A:151 -C:41
6B:1 -C:1
7B:5 -B:16
8B:33 -B:147
9B:41 -D:151
10B:151 -D:41
11C:5 -C:16
12C:33 -C:147
13D:5 -D:16
14D:33 -D:147

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Ala A:80 -Pro A:81
2Glu A:113 -Pro A:114
3Gly A:117 -Pro A:118
4Ala B:80 -Pro B:81
5Glu B:113 -Pro B:114
6Gly B:117 -Pro B:118
7Ala C:80 -Pro C:81
8Glu C:113 -Pro C:114
9Gly C:117 -Pro C:118
10Ala D:80 -Pro D:81
11Glu D:113 -Pro D:114
12Gly D:117 -Pro D:118

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ALU)

(-) 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:157
 aligned with Q7M4F9_CUCEC | Q7M4F9 from UniProtKB/TrEMBL  Length:157

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
         Q7M4F9_CUCEC     1 CLTSCPPLWTGFNGKCFRLFHNHLNFDNAENACRQFGLASCSGDELATGHLASIHSAESQAFLTELVKTSLPDLITGGWAPQVYIGMKVGSTNSDQTWTDGSSVDYDGWVSGEPNNGPNSRGAIAAGDYSRGFWADVYSNNNFKYICQLPCVHYTLE 157
               SCOP domains d3alua_ A: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eee..eeeeeeeeeehhhhhhhhhh.eeeee....eeee.ee....hhhhhhhhhhhhhhhhhhhh......eeeeeeee......eee.....................eeeeee........eeee.....eeeeee...eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3alu A   1 CLTSCPPLWTGFNGKCFRLFHNHLNFDNAENACRQFGLASCSGDELATGHLASIHSAESQAFLTELVKTSLPDLITGGWAPQVYIGMKVGSTNSDQTWTDGSSVDYDGWVSGEPNNGPNSRGAIAAGDYSRGFWADVYSNNNFKYICQLPCVHYTLE 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       


Chain B from PDB  Type:PROTEIN  Length:157
 aligned with Q7M4F9_CUCEC | Q7M4F9 from UniProtKB/TrEMBL  Length:157

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
         Q7M4F9_CUCEC     1 CLTSCPPLWTGFNGKCFRLFHNHLNFDNAENACRQFGLASCSGDELATGHLASIHSAESQAFLTELVKTSLPDLITGGWAPQVYIGMKVGSTNSDQTWTDGSSVDYDGWVSGEPNNGPNSRGAIAAGDYSRGFWADVYSNNNFKYICQLPCVHYTLE 157
               SCOP domains d3alub_ B: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....eee..eeeeeeeeeehhhhhhhhhh..eeee....eeee.ee....hhhhhhhhhhhhhhhhhhhh......eeeeeeee......eee.....................eeeeee........eeee.....eeeeee...eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3alu B   1 CLTSCPPLWTGFNGKCFRLFHNHLNFDNAENACRQFGLASCSGDELATGHLASIHSAESQAFLTELVKTSLPDLITGGWAPQVYIGMKVGSTNSDQTWTDGSSVDYDGWVSGEPNNGPNSRGAIAAGDYSRGFWADVYSNNNFKYICQLPCVHYTLE 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       


Chain C from PDB  Type:PROTEIN  Length:157
 aligned with Q7M4F9_CUCEC | Q7M4F9 from UniProtKB/TrEMBL  Length:157

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
         Q7M4F9_CUCEC     1 CLTSCPPLWTGFNGKCFRLFHNHLNFDNAENACRQFGLASCSGDELATGHLASIHSAESQAFLTELVKTSLPDLITGGWAPQVYIGMKVGSTNSDQTWTDGSSVDYDGWVSGEPNNGPNSRGAIAAGDYSRGFWADVYSNNNFKYICQLPCVHYTLE 157
               SCOP domains d3aluc_ C: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....eee..eeeeeeeeeehhhhhhhhhh..eeee....eeee.ee....hhhhhhhhhhhhhhhhhhhh......eeeeeeee......eee.....................eeeeee........eeee.....eeeeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3alu C   1 CLTSCPPLWTGFNGKCFRLFHNHLNFDNAENACRQFGLASCSGDELATGHLASIHSAESQAFLTELVKTSLPDLITGGWAPQVYIGMKVGSTNSDQTWTDGSSVDYDGWVSGEPNNGPNSRGAIAAGDYSRGFWADVYSNNNFKYICQLPCVHYTLE 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       


Chain D from PDB  Type:PROTEIN  Length:157
 aligned with Q7M4F9_CUCEC | Q7M4F9 from UniProtKB/TrEMBL  Length:157

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
         Q7M4F9_CUCEC     1 CLTSCPPLWTGFNGKCFRLFHNHLNFDNAENACRQFGLASCSGDELATGHLASIHSAESQAFLTELVKTSLPDLITGGWAPQVYIGMKVGSTNSDQTWTDGSSVDYDGWVSGEPNNGPNSRGAIAAGDYSRGFWADVYSNNNFKYICQLPCVHYTLE 157
               SCOP domains d3alud_ D: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....eee..eeeeeeeeeehhhhhhhhhh..eeee....eeee.ee....hhhhhhhhhhhhhhhhhhhh......eeeeeeee......eee.....................eeeeee........eeee.....eeeeee...eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3alu D   1 CLTSCPPLWTGFNGKCFRLFHNHLNFDNAENACRQFGLASCSGDELATGHLASIHSAESQAFLTELVKTSLPDLITGGWAPQVYIGMKVGSTNSDQTWTDGSSVDYDGWVSGEPNNGPNSRGAIAAGDYSRGFWADVYSNNNFKYICQLPCVHYTLE 157
                                    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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q7M4F9_CUCEC | Q7M4F9)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  Cis Peptide Bonds
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  3alu
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 Related Entries

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

UniProtKB/TrEMBL
        Q7M4F9_CUCEC | Q7M4F9: 3als 3alt

(-) Related Entries Specified in the PDB File

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