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(-) Description

Title :  CRYSTAL STRUCTURE OF SLL-2
 
Authors :  A. Kita, M. Jimbo, R. Sakai, Y. Morimoto, K. Miki
Date :  22 Nov 13  (Deposition) - 14 Jan 15  (Release) - 23 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Six-Stranded Antiparallel-Beta Sandwich, Galactose Binding Protein, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kita, M. Jimbo, R. Sakai, Y. Morimoto, K. Miki
Crystal Structure Of A Symbiosis-Related Lectin From Octocoral.
Glycobiology V. 25 1016 2015
PubMed-ID: 26022515  |  Reference-DOI: 10.1093/GLYCOB/CWV033

(-) Compounds

Molecule 1 - GALACTOSE-BINDING LECTIN
    Chains: A, B, C, D, E, F
    Fragment: UNP RESIDUES 47-140
    Organism Scientific: SINULARIA LOCHMODES
    Organism Taxid: 301888

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 35)

Asymmetric/Biological Unit (6, 35)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2CL12Ligand/IonCHLORIDE ION
3GLA1Ligand/IonALPHA D-GALACTOSE
4MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5NA6Ligand/IonSODIUM ION
6NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:56 , ARG A:58 , TRP A:78 , TRP B:18 , ASP B:50 , TRP B:84BINDING SITE FOR RESIDUE MPD A 103
02AC2SOFTWAREASN A:55 , ASN A:56 , ARG A:58 , THR A:80BINDING SITE FOR RESIDUE CL A 104
03AC3SOFTWAREARG A:16 , NAG C:102BINDING SITE FOR RESIDUE CL A 105
04AC4SOFTWAREHIS A:15 , CYS A:17BINDING SITE FOR RESIDUE NA A 106
05AC5SOFTWAREASN B:55 , ASN B:56 , ARG B:58 , THR B:80BINDING SITE FOR RESIDUE CL B 103
06AC6SOFTWARENAG A:101 , ARG B:16BINDING SITE FOR RESIDUE CL B 104
07AC7SOFTWAREASN B:56 , ARG B:58 , TRP B:78 , TYR B:79 , TRP C:18 , ASP C:50 , TRP C:84BINDING SITE FOR RESIDUE A2G C 101
08AC8SOFTWAREHIS B:15 , CYS B:17BINDING SITE FOR RESIDUE NA B 105
09AC9SOFTWARETRP A:18 , ASP A:50 , TRP A:84 , ASN C:56 , ARG C:58 , TRP C:78BINDING SITE FOR RESIDUE MPD C 104
10BC1SOFTWAREASN C:55 , ASN C:56 , ARG C:58 , THR C:80BINDING SITE FOR RESIDUE CL C 105
11BC2SOFTWARENAG B:101 , ARG C:16BINDING SITE FOR RESIDUE CL C 106
12BC3SOFTWAREASP C:23 , HOH C:220BINDING SITE FOR RESIDUE NA C 107
13BC4SOFTWARETRP D:18 , ASP D:50 , TRP D:84 , ASN E:56 , ARG E:58 , TRP E:78BINDING SITE FOR RESIDUE MPD D 103
14BC5SOFTWAREASN D:55 , ASN D:56 , ARG D:58 , THR D:80BINDING SITE FOR RESIDUE CL D 104
15BC6SOFTWAREARG D:16 , NAG E:101BINDING SITE FOR RESIDUE CL D 105
16BC7SOFTWAREHIS D:15 , CYS D:17BINDING SITE FOR RESIDUE NA D 106
17BC8SOFTWAREASN E:55 , ASN E:56 , ARG E:58 , THR E:80BINDING SITE FOR RESIDUE CL E 103
18BC9SOFTWAREARG E:16 , MET E:48 , NAG F:101BINDING SITE FOR RESIDUE CL E 104
19CC1SOFTWARECYS E:17 , ASP E:23BINDING SITE FOR RESIDUE NA E 105
20CC2SOFTWAREASN D:56 , ARG D:58 , TRP D:78 , TYR D:79 , TRP F:18 , ASP F:50 , TRP F:84BINDING SITE FOR RESIDUE GLA F 103
21CC3SOFTWAREASN F:55 , ASN F:56 , ARG F:58 , THR F:80BINDING SITE FOR RESIDUE CL F 104
22CC4SOFTWARENAG D:101 , ARG F:16BINDING SITE FOR RESIDUE CL F 105
23CC5SOFTWARECYS F:17 , ASP F:23BINDING SITE FOR RESIDUE NA F 106
24CC6SOFTWAREASN A:60 , SER A:62 , ASP A:64 , HIS A:74 , ASN A:76 , ARG B:16 , CL B:104BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 60 RESIDUES 101 TO 102
25CC7SOFTWAREASN B:60 , SER B:62 , ASP B:64 , HIS B:74 , ASN B:76 , TRP B:78 , ARG C:16 , CL C:106BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 60 RESIDUES 101 TO 102
26CC8SOFTWAREARG A:16 , CL A:105 , ASN C:60 , SER C:62 , ASP C:64 , HIS C:74 , ASN C:76 , TRP C:78BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 60 RESIDUES 102 TO 103
27CC9SOFTWAREASN D:60 , SER D:62 , ASP D:64 , HIS D:74 , ASN D:76 , TRP D:78 , ARG F:16 , CL F:105BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 60 RESIDUES 101 TO 102
28DC1SOFTWAREARG D:16 , CL D:105 , ASN E:60 , SER E:62 , ASP E:64 , HIS E:74 , ASN E:76 , TRP E:78BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E 60 RESIDUES 101 TO 102
29DC2SOFTWAREARG E:16 , CL E:104 , ASN F:60 , SER F:62 , ASP F:64 , HIS F:74 , ASN F:76 , TRP F:78BINDING SITE FOR CHAIN F OF SUGAR BOUND TO ASN F 60 RESIDUES 101 TO 102

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:8 -A:93
2A:17 -A:22
3B:8 -B:93
4B:17 -B:22
5C:8 -C:93
6C:17 -C:22
7D:8 -D:93
8D:17 -D:22
9E:8 -E:93
10E:17 -E:22
11F:8 -F:93
12F:17 -F:22

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Trp A:18 -Pro A:19
2Trp A:33 -Pro A:34
3Trp B:18 -Pro B:19
4Trp B:33 -Pro B:34
5Trp C:18 -Pro C:19
6Trp C:33 -Pro C:34
7Trp D:18 -Pro D:19
8Trp D:33 -Pro D:34
9Trp E:18 -Pro E:19
10Trp E:33 -Pro E:34
11Trp F:18 -Pro F:19
12Trp F:33 -Pro F:34

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WMP)

(-) 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:94
                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeeeeeee........eeeeeee.........eeeeeeeeeee.....eeeeeeee.....eeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  3wmp A  1 RLIHVSRCEMGTSTHRCWPRPCDTSSDEPISFWPPFENTPNVIVSFGMLDVDNSNNLRVNSSADDVTVGGFTLHYNSWYTTTVWNYKLIWIACD 94
                                    10        20        30        40        50        60        70        80        90    


Chain B from PDB  Type:PROTEIN  Length:94
                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeeeeeee........eeeeeee.........eeeeeeeeeee.....eeeeeeeeeee..eeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  3wmp B  1 RLIHVSRCEMGTSTHRCWPRPCDTSSDEPISFWPPFENTPNVIVSFGMLDVDNSNNLRVNSSADDVTVGGFTLHYNSWYTTTVWNYKLIWIACD 94
                                    10        20        30        40        50        60        70        80        90    


Chain C from PDB  Type:PROTEIN  Length:94
                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeeeeeee........eeeeeee.........eeeeeeeeeee.....eeeeeeeeeee..eeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  3wmp C  1 RLIHVSRCEMGTSTHRCWPRPCDTSSDEPISFWPPFENTPNVIVSFGMLDVDNSNNLRVNSSADDVTVGGFTLHYNSWYTTTVWNYKLIWIACD 94
                                    10        20        30        40        50        60        70        80        90    


Chain D from PDB  Type:PROTEIN  Length:94
                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeeeeeee........eeeeeee.........eeeeeeeeeee.....eeeeeeeeeee..eeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  3wmp D  1 RLIHVSRCEMGTSTHRCWPRPCDTSSDEPISFWPPFENTPNVIVSFGMLDVDNSNNLRVNSSADDVTVGGFTLHYNSWYTTTVWNYKLIWIACD 94
                                    10        20        30        40        50        60        70        80        90    


Chain E from PDB  Type:PROTEIN  Length:94
                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeeeeeee........eeeeeee.........eeeeeeeeeee.....eeeeeeee.....eeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  3wmp E  1 RLIHVSRCEMGTSTHRCWPRPCDTSSDEPISFWPPFENTPNVIVSFGMLDVDNSNNLRVNSSADDVTVGGFTLHYNSWYTTTVWNYKLIWIACD 94
                                    10        20        30        40        50        60        70        80        90    


Chain F from PDB  Type:PROTEIN  Length:94
                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeeeeeee........eeeeeee.........eeeeeeeeeee.....eeeeeeeeeee..eeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  3wmp F  1 RLIHVSRCEMGTSTHRCWPRPCDTSSDEPISFWPPFENTPNVIVSFGMLDVDNSNNLRVNSSADDVTVGGFTLHYNSWYTTTVWNYKLIWIACD 94
                                    10        20        30        40        50        60        70        80        90
   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  (0, 0)

(no "SCOP Domain" information available for 3WMP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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        A4CYJ6_9CNID | A4CYJ6: 3wmq

(-) Related Entries Specified in the PDB File

3wmq