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(-) Description

Title :  CRYSTAL STRUCTURES OF NOVEL MONOMERIC MONOCOT MANNOSE-BINDING LECTINS FROM GASTRODIA ELATA
 
Authors :  W. Liu, N. Yang, M. Wang, R. H. Huang, Z. Hu, D. C. Wang
Date :  04 Sep 04  (Deposition) - 11 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A,B  (1x)
Keywords :  Monocot Mannose Binding Lectin, Monomer, Homogeneous Beta- Sheet, Antifungal Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Liu, N. Yang, J. Ding, R. H. Huang, Z. Hu, D. C. Wang
Structural Mechanism Governing The Quaternary Organization Of Monocot Mannose-Binding Lectin Revealed By The Novel Monomeric Structure Of An Orchid Lectin
J. Biol. Chem. V. 280 14865 2005
PubMed-ID: 15649901  |  Reference-DOI: 10.1074/JBC.M411634200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTIFUNGAL PROTEIN GAFP-1
    Chains: A, B, C, D
    Fragment: RESIDUES 1-112
    Organism Scientific: GASTRODIA ELATA
    Organism Taxid: 91201
    Synonym: GASTRODIANIN-1
    Tissue: CORMS

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 5 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:46 , GLY A:47 , HOH A:1054 , HOH A:1070 , ARG B:38 , ARG B:91BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWAREARG A:38 , ARG A:91 , HOH A:1078 , ASN B:46 , GLY B:47BINDING SITE FOR RESIDUE SO4 A 1002

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:29 -A:52
2B:29 -B:52
3C:29 -C:52
4D:29 -D:52

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XD5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XD5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XD5)

(-) Exons   (0, 0)

(no "Exon" information available for 1XD5)

(-) 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:112
 aligned with Q9AXZ2_9ASPA | Q9AXZ2 from UniProtKB/TrEMBL  Length:179

    Alignment length:112
                                    38        48        58        68        78        88        98       108       118       128       138  
         Q9AXZ2_9ASPA    29 SDRLNSGHQLDTGGSLAQGGYLFIIQNDCNLVLYDNNRAVWASGTNGKASGCVLKMQNDGNLVIYSGSRAIWASNTNRQNGNYYLILQRDRNVVIYDNSNNAIWATHTNVGN 140
               SCOP domains d1xd5a_ A: Gastrodianin (antifungal protein)                                                                     SCOP domains
               CATH domains 1xd5A00 A:1-112 Agglutinin, subunit A                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee....eeee..eeeee.....eeeee..eeeee.........eeeee.....eeeee..eeeee..........eeee.....eeee.....eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1xd5 A   1 SDRLNSGHQLDTGGSLAEGGYLFIIQNDCNLVLYDNNRAVWASGTNGKASGCVLKMQNDGNLVIYSGSRAIWASNTNRQNGNYYLILQRDRNVVIYDNSNNAIWATHTNVGN 112
                                    10        20        30        40        50        60        70        80        90       100       110  


Chain B from PDB  Type:PROTEIN  Length:112
 aligned with Q9AXZ2_9ASPA | Q9AXZ2 from UniProtKB/TrEMBL  Length:179

    Alignment length:112
                                    38        48        58        68        78        88        98       108       118       128       138  
         Q9AXZ2_9ASPA    29 SDRLNSGHQLDTGGSLAQGGYLFIIQNDCNLVLYDNNRAVWASGTNGKASGCVLKMQNDGNLVIYSGSRAIWASNTNRQNGNYYLILQRDRNVVIYDNSNNAIWATHTNVGN 140
               SCOP domains d1xd5b_ B: Gastrodianin (antifungal protein)                                                                     SCOP domains
               CATH domains 1xd5B00 B:1-112 Agglutinin, subunit A                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee....eeee..eeeee.....eeeee..eeeee..........eeee.....eeeee..eeeee..........eeee.....eeee.....eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1xd5 B   1 SDRLNSGHQLDTGGSLAEGGYLFIIQNDCNLVLYDNNRAVWASGTNGKASGCVLKMQNDGNLVIYSGSRAIWASNTNRQNGNYYLILQRDRNVVIYDNSNNAIWATHTNVGN 112
                                    10        20        30        40        50        60        70        80        90       100       110  


Chain C from PDB  Type:PROTEIN  Length:111
 aligned with Q9AXZ2_9ASPA | Q9AXZ2 from UniProtKB/TrEMBL  Length:179

    Alignment length:111
                                    38        48        58        68        78        88        98       108       118       128       138 
         Q9AXZ2_9ASPA    29 SDRLNSGHQLDTGGSLAQGGYLFIIQNDCNLVLYDNNRAVWASGTNGKASGCVLKMQNDGNLVIYSGSRAIWASNTNRQNGNYYLILQRDRNVVIYDNSNNAIWATHTNVG 139
               SCOP domains d1xd5c_ C: Gastrodianin (antifungal protein)                                                                    SCOP domains
               CATH domains 1xd5C00 C:1-111 Agglutinin, subunit A                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee....eeee..eeeee.....eeeee..eeeee.........eeeee.....eeeee..eeeee..........eeee.....eeee.....eeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 1xd5 C   1 SDRLNSGHQLDTGGSLAEGGYLFIIQNDCNLVLYDNNRAVWASGTNGKASGCVLKMQNDGNLVIYSGSRAIWASNTNRQNGNYYLILQRDRNVVIYDNSNNAIWATHTNVG 111
                                    10        20        30        40        50        60        70        80        90       100       110 


Chain D from PDB  Type:PROTEIN  Length:110
 aligned with Q9AXZ2_9ASPA | Q9AXZ2 from UniProtKB/TrEMBL  Length:179

    Alignment length:110
                                    38        48        58        68        78        88        98       108       118       128       138
         Q9AXZ2_9ASPA    29 SDRLNSGHQLDTGGSLAQGGYLFIIQNDCNLVLYDNNRAVWASGTNGKASGCVLKMQNDGNLVIYSGSRAIWASNTNRQNGNYYLILQRDRNVVIYDNSNNAIWATHTNV 138
               SCOP domains d1xd5d_ D: Gastrodianin (antifungal protein)                                                                   SCOP domains
               CATH domains 1xd5D00 D:1-110 Agglutinin, subunit A                                                                          CATH domains
           Pfam domains (1) --B_lectin-1xd5D01 D:3-110                                                                                     Pfam domains (1)
           Pfam domains (2) --B_lectin-1xd5D02 D:3-110                                                                                     Pfam domains (2)
           Pfam domains (3) --B_lectin-1xd5D03 D:3-110                                                                                     Pfam domains (3)
           Pfam domains (4) --B_lectin-1xd5D04 D:3-110                                                                                     Pfam domains (4)
         Sec.struct. author ..eee..eee....eeee..eeeee.....eeeee..eeeee.........eeeee.....eeeee..eeeee..........eeee.....eeee.....eeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1xd5 D   1 SDRLNSGHQLDTGGSLAEGGYLFIIQNDCNLVLYDNNRAVWASGTNGKASGCVLKMQNDGNLVIYSGSRAIWASNTNRQNGNYYLILQRDRNVVIYDNSNNAIWATHTNV 110
                                    10        20        30        40        50        60        70        80        90       100       110
   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  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1XD5)

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1xd6 QUATERNARY STATES OF MONOCOT MANNOSE-BINDING LECTINS