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(-) Description

Title :  MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM GARLIC (ALLIUM SATIVUM) BULBS COMPLEXED WITH ALPHA-D-MANNOSE
 
Authors :  G. Ramachandraiah, N. R. Chandra, A. Surolia, M. Vijayan
Date :  04 Dec 01  (Deposition) - 22 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,D,P,Q
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  P,Q  (1x)
Keywords :  Bulb Lectin, Mannose, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Ramachandraiah, N. R. Chandra, A. Surolia, M. Vijayan
Re-Refinement Using Reprocessed Data To Improve The Quality Of The Structure: A Case Study Involving Garlic Lectin.
Acta Crystallogr. , Sect. D V. 58 414 2002
PubMed-ID: 11856826  |  Reference-DOI: 10.1107/S0907444901021497
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LECTIN I
    Chains: A, P
    Organism Common: GARLIC
    Organism Scientific: ALLIUM SATIVUM
    Organism Taxid: 4682
    Synonym: MANNOSE-SPECIFIC AGGLUTININ;
LECGNA 1
 
Molecule 2 - LECTIN II
    Chains: D, Q
    Organism Common: GARLIC
    Organism Scientific: ALLIUM SATIVUM
    Organism Taxid: 4682
    Synonym: MANNOSE-SPECIFIC AGGLUTININ;
LECGNA 2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ADPQ
Biological Unit 1 (1x): AD  
Biological Unit 2 (1x):   PQ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1MAN14Ligand/IonALPHA-D-MANNOSE
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1MAN7Ligand/IonALPHA-D-MANNOSE
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
1MAN7Ligand/IonALPHA-D-MANNOSE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:90 , ASP A:92 , ASN A:94 , TYR A:98 , ASN D:84 , ASP D:101 , SER D:104BINDING SITE FOR RESIDUE MAN A 300
02AC2SOFTWAREGLN A:58 , ASP A:60 , ASN A:62 , TYR A:66 , SER A:72 , HIS A:77BINDING SITE FOR RESIDUE MAN A 301
03AC3SOFTWAREGLN A:26 , ASP A:28 , ASN A:30 , TYR A:34 , HOH A:421 , HOH D:563BINDING SITE FOR RESIDUE MAN A 302
04AC4SOFTWARETYR A:21 , ASP A:35 , THR A:38 , SER A:39 , VAL A:40 , GLY A:93 , THR D:107 , LYS D:109BINDING SITE FOR RESIDUE MAN A 303
05AC5SOFTWAREASN A:84 , ASP A:101 , SER A:104 , TYR A:108 , GLN D:90 , ASP D:92 , ASN D:94 , TYR D:98BINDING SITE FOR RESIDUE MAN D 304
06AC6SOFTWAREGLN D:58 , ASP D:60 , ASN D:62 , TYR D:66 , SER D:72 , HOH D:514BINDING SITE FOR RESIDUE MAN D 305
07AC7SOFTWAREGLN D:26 , ASP D:28 , ASN D:30 , TYR D:34 , ASP D:46 , HOH D:407 , LYS P:50 , ARG P:71BINDING SITE FOR RESIDUE MAN D 306
08AC8SOFTWAREGLN P:90 , ASP P:92 , ASN P:94 , TYR P:98 , MET Q:5 , ASN Q:84 , ASP Q:101 , HOH Q:417BINDING SITE FOR RESIDUE MAN P 307
09AC9SOFTWAREGLN P:58 , ASP P:60 , ASN P:62 , TYR P:66BINDING SITE FOR RESIDUE MAN P 308
10BC1SOFTWAREGLN P:26 , ASP P:28 , ASN P:30 , TYR P:34 , SER P:39 , ALA Q:68 , GLU Q:69 , HOH Q:544BINDING SITE FOR RESIDUE MAN P 309
11BC2SOFTWARETYR P:21 , LEU P:33 , ASP P:35 , VAL P:40 , GLY P:93 , HOH P:438 , ALA Q:12 , GLY Q:13 , THR Q:107 , LYS Q:109BINDING SITE FOR RESIDUE MAN P 310
12BC3SOFTWAREASN P:84 , ASP P:101 , TYR P:108 , GLN Q:90 , ASP Q:92 , ASN Q:94 , TYR Q:98 , HOH Q:486BINDING SITE FOR RESIDUE MAN Q 311
13BC4SOFTWAREGLN Q:58 , ASP Q:60 , ASN Q:62 , TYR Q:66 , SER Q:72 , HOH Q:441BINDING SITE FOR RESIDUE MAN Q 312
14BC5SOFTWAREILE A:47 , LYS A:50 , ARG A:71 , GLN Q:26 , ASP Q:28 , ASN Q:30 , TYR Q:34 , ASP Q:46 , HOH Q:449BINDING SITE FOR RESIDUE MAN Q 313

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:29 -A:53
2D:29 -D:53
3P:29 -P:53
4Q:29 -Q:53

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu D:19 -Pro D:20

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KJ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KJ1)

(-) Exons   (0, 0)

(no "Exon" information available for 1KJ1)

(-) Sequences/Alignments

Asymmetric 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:109
 aligned with Q38789_ALLSA | Q38789 from UniProtKB/TrEMBL  Length:303

    Alignment length:109
                                   186       196       206       216       226       236       246       256       266       276         
         Q38789_ALLSA   177 RNILRNDEGLYAGQSLDVEPYHFIMQEDCNLVLYDHSTAVWASNTDIPGKKGCKAVLQSDGNFVVYDAEGRSLWASHSVRGNGNYVLVLQEDGNVVIYGSDIWSTDTYR 285
               SCOP domains d1kj1a_ A: Lectin (agglutinin)                                                                                SCOP domains
               CATH domains 1kj1A00 A:1-109 Agglutinin, subunit A                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee...eeee..eeeee.....eeeee..eeeee...........eeee.....eeee.....eeee..........eeee.....eeee..eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1kj1 A   1 RNLLTNGEGLYAGQSLDVEPYHFIMQEDCNLVLYDHSTSVWASNTGILGKKGCKAVLQSDGNFVVYDAEGRSLWASHSVRGNGNYVLVLQEDGNVVIYGSDIWSTGTYK 109
                                    10        20        30        40        50        60        70        80        90       100         


Chain D from PDB  Type:PROTEIN  Length:109
 aligned with Q38783_ALLSA | Q38783 from UniProtKB/TrEMBL  Length:155

    Alignment length:109
                                    38        48        58        68        78        88        98       108       118       128         
         Q38783_ALLSA    29 RNILMNDEGLYAGQSLDVEPYHLIMQEDCNLVLYDHSTAVWTSNTDIPGKKGCKAVLQSDGNFVVYDAEGRSLWASHSVRGNGNYVLVLQEDGNVVIYGSDIWSTNTYK 137
               SCOP domains d1kj1d_ D: Lectin (agglutinin)                                                                                SCOP domains
               CATH domains 1kj1D00 D:1-109 Agglutinin, subunit A                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee...eeee..eeeee.....eeeee..eeeee...........eeee.....eeee.....eeee.........eeeee.....eeeee.eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1kj1 D   1 RNILMNDEGLYAGQSLDVEPYHLIMQEDCNLVLYDHSTAVWTTNTDIPGKKGCKAVLQSDGNFVVYDAEGRSLWASHSVRGNGNYVLVLQEDGNVVIYGSDIWSTNTYK 109
                                    10        20        30        40        50        60        70        80        90       100         


Chain P from PDB  Type:PROTEIN  Length:109
 aligned with Q38789_ALLSA | Q38789 from UniProtKB/TrEMBL  Length:303

    Alignment length:109
                                   186       196       206       216       226       236       246       256       266       276         
         Q38789_ALLSA   177 RNILRNDEGLYAGQSLDVEPYHFIMQEDCNLVLYDHSTAVWASNTDIPGKKGCKAVLQSDGNFVVYDAEGRSLWASHSVRGNGNYVLVLQEDGNVVIYGSDIWSTDTYR 285
               SCOP domains d1kj1p_ P: Lectin (agglutinin)                                                                                SCOP domains
               CATH domains 1kj1P00 P:1-109 Agglutinin, subunit A                                                                         CATH domains
           Pfam domains (1) ----B_lectin-1kj1P01 P:5-108                                                                                - Pfam domains (1)
           Pfam domains (2) ----B_lectin-1kj1P02 P:5-108                                                                                - Pfam domains (2)
         Sec.struct. author ..eee...eee...eeee..eeeee.....eeeee..eeeee...........eeee.....eeee.....eeee.........eeeee.....eeeee.eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1kj1 P   1 RNLLTNGEGLYAGQSLDVEPYHFIMQEDCNLVLYDHSTSVWASNTGILGKKGCKAVLQSDGNFVVYDAEGRSLWASHSVRGNGNYVLVLQEDGNVVIYGSDIWSTGTYK 109
                                    10        20        30        40        50        60        70        80        90       100         


Chain Q from PDB  Type:PROTEIN  Length:109
 aligned with Q38783_ALLSA | Q38783 from UniProtKB/TrEMBL  Length:155

    Alignment length:109
                                    38        48        58        68        78        88        98       108       118       128         
         Q38783_ALLSA    29 RNILMNDEGLYAGQSLDVEPYHLIMQEDCNLVLYDHSTAVWTSNTDIPGKKGCKAVLQSDGNFVVYDAEGRSLWASHSVRGNGNYVLVLQEDGNVVIYGSDIWSTNTYK 137
               SCOP domains d1kj1q_ Q: Lectin (agglutinin)                                                                                SCOP domains
               CATH domains 1kj1Q00 Q:1-109 Agglutinin, subunit A                                                                         CATH domains
           Pfam domains (1) B_lectin-1kj1Q01 Q:1-109                                                                                      Pfam domains (1)
           Pfam domains (2) B_lectin-1kj1Q02 Q:1-109                                                                                      Pfam domains (2)
         Sec.struct. author ..eee...eee...eeee..eeeee.....eeeee..eeeee...........eeee.....eeee.....eeee.........eeeee.....eeeee.eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1kj1 Q   1 RNILMNDEGLYAGQSLDVEPYHLIMQEDCNLVLYDHSTAVWTTNTDIPGKKGCKAVLQSDGNFVVYDAEGRSLWASHSVRGNGNYVLVLQEDGNVVIYGSDIWSTNTYK 109
                                    10        20        30        40        50        60        70        80        90       100
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: B_lectin] (7)

(-) Gene Ontology  (1, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,P   (Q38789_ALLSA | Q38789)
molecular function
    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.

Chain D,Q   (Q38783_ALLSA | Q38783)
molecular function
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q38789_ALLSA | Q38789: 1bwu

(-) Related Entries Specified in the PDB File

1bwu