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(-) Description

Title :  X-RAY STRUCTURAL ANALYSIS OF A MANNOSE SPECIFIC LECTIN FROM DUTCH CROCUS (CROCUS VERNUS)
 
Authors :  A. Akrem, A. Meyer, M. Perbandt, W. Voelter, F. Buck, C. Betzel
Date :  01 Apr 10  (Deposition) - 22 Jun 11  (Release) - 22 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Lectin, Crocus, Heterotetramer, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Akrem
X-Ray Structural Analysis Of A Mannose Specific Lectin From Dutch Crocus (Crocus Vernus)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MANNOSE-SPECIFIC LECTIN 3 CHAIN 1
    Chains: A, C
    Organism Common: DUTCH CROCUS
    Organism Scientific: CROCUS VERNUS
    Organism Taxid: 87752
    Other Details: BULB
 
Molecule 2 - MANNOSE-SPECIFIC LECTIN 3 CHAIN 2
    Chains: B, D
    Organism Common: DUTCH CROCUS
    Organism Scientific: CROCUS VERNUS
    Organism Taxid: 87752
    Other Details: BULB

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1FMT8Ligand/IonFORMIC ACID
2GOL3Ligand/IonGLYCEROL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:93 , ASP A:94 , HOH A:131 , HOH A:200 , ILE B:2BINDING SITE FOR RESIDUE GOL A 112
02AC2SOFTWAREHOH A:418 , HOH A:578 , ARG B:24 , ASP B:25 , LYS B:40 , HOH B:323BINDING SITE FOR RESIDUE GOL A 113
03AC3SOFTWAREGLU A:20 , HOH A:130 , PRO B:3BINDING SITE FOR RESIDUE FMT A 114
04AC4SOFTWAREGLU A:20 , HOH A:320BINDING SITE FOR RESIDUE FMT A 115
05AC5SOFTWAREGLY B:56 , GLN B:57 , HIS B:58 , ASP B:73 , ASP B:74BINDING SITE FOR RESIDUE FMT B 114
06AC6SOFTWAREASN A:86 , GLN B:96 , TYR B:104BINDING SITE FOR RESIDUE FMT B 116
07AC7SOFTWAREPRO C:93 , ASP C:94 , HOH C:153 , ILE D:2 , PHE D:10 , HOH D:124BINDING SITE FOR RESIDUE GOL C 112
08AC8SOFTWARESER C:66 , SER C:69 , HOH C:534BINDING SITE FOR RESIDUE FMT C 113
09AC9SOFTWAREGLY D:56 , GLN D:57 , HIS D:58 , ASP D:73 , ASP D:74BINDING SITE FOR RESIDUE FMT D 114
10BC1SOFTWAREHOH C:153 , HIS D:65 , ASP D:90 , HOH D:188 , HOH D:275 , HOH D:580BINDING SITE FOR RESIDUE FMT D 115

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:30 -A:52
2B:34 -B:59
3C:30 -C:52
4D:34 -D:59

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Tyr A:76 -Pro A:77
2Gly A:101 -Pro A:102
3Ala A:110 -Ala A:111
4Gly B:105 -Pro B:106
5Ala B:112 -Ala B:113
6Tyr C:76 -Pro C:77
7Gly C:101 -Pro C:102
8Ala C:109 -Ala C:110
9Gly D:105 -Pro D:106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BULB_LECTINPS50927 Bulb-type lectin domain profile.LEC3_CROVR2-112
 
117-224
 		  4A:2-111
C:2-110
B:6-113
D:6-112

(-) Exons   (0, 0)

(no "Exon" information available for 3MEZ)

(-) 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:111
 aligned with LEC3_CROVR | P86626 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:111
                                    10        20        30        40        50        60        70        80        90       100       110 
           LEC3_CROVR     1 DNNVLLTGDVIHTDNQLSYESAAFVMQGDCNLVLYNEAGGFQSNTHGRGVDCTLRLNNRGQLEIHSANSNTPVWVYPRSVNTVRGNYAATLGPDQHVTIYGPAIWSTPAAA 111
               SCOP domains d3meza_ A: automated matches                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...ee....eeee..eeeee.....eeee.....ee..........eeee.....eeee........eee...........eeee.....eeee..eeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -BULB_LECTIN  PDB: A:2-111 UniProt: 2-112                                                                       PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 3mez A   1 DNNVLLTGDVIHTDNQLSYESAAFVMQGDCNLVLYNEAGGFQSNTHGRGVDCTLRLNNRGQLEIHSANSNTPVWVYPRSVNTVRGNYAATLGPDQHVTIYGPAIWSTPAAA 111
                                    10        20        30        40        50        60        70        80        90       100       110 


Chain B from PDB  Type:PROTEIN  Length:113
 aligned with LEC3_CROVR | P86626 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:113
                                   121       131       141       151       161       171       181       191       201       211       221   
           LEC3_CROVR   112 NIPRVRNVLFSSQVMYDNAQLATRDYSLVMRDDCNLVLTKGSKTNIVWESGTSGRGQHCFMRLGHSGELDITDDRLNTVFVSNTVGQEGDYVLILQINGQAVVYGPAVWSTAA 224
               SCOP domains d3mezb_ B: automated matches                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- 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 B----BULB_LECTIN  PDB: B:6-113 UniProt: 117-224                                                                   PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 3mez B   1 NIPRVRNVLFSSQVMYDNAQLATRDYSLVMRDDCNLVLTKGSKTNIVWESGTSGRGQHCFMRLGHSGELDITDDRLNTVFVSNTVGQEGDYVLILQINGQAVVYGPAVWSTAA 113
                                    10        20        30        40        50        60        70        80        90       100       110   


Chain C from PDB  Type:PROTEIN  Length:110
 aligned with LEC3_CROVR | P86626 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:110
                                    10        20        30        40        50        60        70        80        90       100       110
           LEC3_CROVR     1 DNNVLLTGDVIHTDNQLSYESAAFVMQGDCNLVLYNEAGGFQSNTHGRGVDCTLRLNNRGQLEIHSANSNTPVWVYPRSVNTVRGNYAATLGPDQHVTIYGPAIWSTPAA 110
               SCOP domains d3mezc_ C: automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...ee....eeee..eeeee.....eeee.....ee..........eeee.....eeee........eee...........eeee.....eeee..eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -BULB_LECTIN  PDB: C:2-110 UniProt: 2-112                                                                      PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 3mez C   1 DNNVLLTGDVIHTDNQLSYESAAFVMQGDCNLVLYNEAGGFQSNTHGRGVDCTLRLNNRGQLEIHSANSNTPVWVYPRSVNTVRGNYAATLGPDQHVTIYGPAIWSTPAA 110
                                    10        20        30        40        50        60        70        80        90       100       110


Chain D from PDB  Type:PROTEIN  Length:112
 aligned with LEC3_CROVR | P86626 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:112
                                   121       131       141       151       161       171       181       191       201       211       221  
           LEC3_CROVR   112 NIPRVRNVLFSSQVMYDNAQLATRDYSLVMRDDCNLVLTKGSKTNIVWESGTSGRGQHCFMRLGHSGELDITDDRLNTVFVSNTVGQEGDYVLILQINGQAVVYGPAVWSTA 223
               SCOP domains d3mezd_ D: automated matches                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---B_lectin-3mezD01 D:4-111                                                                                    - Pfam domains (1)
           Pfam domains (2) ---B_lectin-3mezD02 D:4-111                                                                                    - Pfam domains (2)
           Pfam domains (3) ---B_lectin-3mezD03 D:4-111                                                                                    - Pfam domains (3)
           Pfam domains (4) ---B_lectin-3mezD04 D:4-111                                                                                    - Pfam domains (4)
         Sec.struct. author .......eee...eee...eeee..eeeee.....eeeee....eeeee..........eeee.....eeee.....eeee..........eeee.....eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE B----BULB_LECTIN  PDB: D:6-112 UniProt: 117-224                                                                  PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 3mez D   1 NIPRVRNVLFSSQVMYDNAQLATRDYSLVMRDDCNLVLTKGSKTNIVWESGTSGRGQHCFMRLGHSGELDITDDRLNTVFVSNTVGQEGDYVLILQINGQAVVYGPAVWSTA 112
                                    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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (LEC3_CROVR | P86626)
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.
    GO:0005537    mannose binding    Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.

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(-) Related Entries Specified in the PDB File

1msa MANNOSE SPECIFIC LECTIN FROM GALANTHUS NIVALIS