Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  X-RAY STRUCTURE OF NI, CA CONCANAVALIN A AT ULTRA-HIGH RESOLUTION (0.94A)
 
Authors :  H. U. Ahmed, M. P. Blakeley, M. Cianci, D. W. J. Cruickshank, J. A. Hubbard, J. R. Helliwell
Date :  01 Mar 07  (Deposition) - 31 Jul 07  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.94
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Lectin, Calcium, Manganese, Metal-Binding, Ni (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. U. Ahmed, M. P. Blakeley, M. Cianci, D. W. J. Cruickshank, J. A. Hubbard, J. R. Helliwell
The Determination Of Protonation States In Proteins.
Acta Crystallogr. , Sect. D V. 63 906 2007
PubMed-ID: 17642517  |  Reference-DOI: 10.1107/S0907444907029976

(-) Compounds

Molecule 1 - CONCANAVALIN
    Chains: A
    Organism Common: JACK BEAN
    Organism Scientific: CANAVALIA ENSIFORMIS
    Organism Taxid: 3823
    Synonym: CON A

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2NI1Ligand/IonNICKEL (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:8 , ASP A:10 , ASP A:19 , HIS A:24 , HOH A:1006 , HOH A:1051BINDING SITE FOR RESIDUE NI A 239
2AC2SOFTWAREASP A:10 , TYR A:12 , ASN A:14 , ASP A:19 , HOH A:1255 , HOH A:1276BINDING SITE FOR RESIDUE CA A 240

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2UU8)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Thr A:120 -His A:121
2His A:121 -Glu A:122
3Ala A:207 -Asp A:208

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2UU8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2UU8)

(-) Exons   (0, 0)

(no "Exon" information available for 2UU8)

(-) 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:237
 aligned with CONA_CANEN | P02866 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:238
                                                                                                                      1                                                                                                                                                   
                                     -         -         -         -         -         -         -         -         -|       10        20        30        40        50        60        70        80        90       100       110       120       130       140        
           CONA_CANEN     - ------------------------------------------------------------------------------------------MAISKKSSLFLPIFTFITMFLMVVNKVSSSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 148
               SCOP domains d2uu8a_ A: Concanavalin A                                                                                                                                                                                                                      SCOP domains
               CATH domains 2uu8A00 A:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------Lectin_legB-2uu8A01 A:124-237                                                                                      Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee......eeeeee.hhhhh...eeeeeeeee........eeee-eeeeeeeee.....eeeeeeee.........eeeee..ee.hhh.ee..............eeeeee...ee.....eeeeeeeeeeeee..........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uu8 A   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVDKRLSAVVSYPNADSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILS-WSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       109       119       129       139       149       159       169       179       189       199       209       219       229        
                                                                                                                                     108 |                                                                                                                                
                                                                                                                                       109
   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, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Concanavalin (293)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (CONA_CANEN | P02866)
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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:207 - Asp A:208   [ RasMol ]  
    His A:121 - Glu A:122   [ RasMol ]  
    Thr A:120 - His A:121   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2uu8
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CONA_CANEN | P02866
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  CONA_CANEN | P02866
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CONA_CANEN | P02866: 1apn 1bxh 1c57 1ces 1cjp 1cn1 1con 1cvn 1dq0 1dq1 1dq2 1dq4 1dq5 1dq6 1enq 1enr 1ens 1gic 1gkb 1hqw 1i3h 1jbc 1jn2 1joj 1jui 1jw6 1jyc 1jyi 1nls 1nxd 1ona 1qgl 1qny 1scr 1scs 1tei 1val 1vam 1xqn 2cna 2ctv 2enr 2yz4 3cna 3d4k 3enr 3nwk 4p9w 4p9x 4p9y 4pf5 5cna

(-) Related Entries Specified in the PDB File

1apn MOL_ID: 1; MOLECULE: CONCANAVALIN A; CHAIN: A, B; SYNONYM: CON A; OTHER_DETAILS: DEMETALLIZED, PH 5
1bxh CONCANAVALIN A COMPLEXED TO METHYL ALPHA1-2 MANNOBIOSIDE
1c57 DIRECT DETERMINATION OF THE POSITIONS OF DEUTERIUM ATOMS OF BOUND WATER IN CONCANAVALIN A BY NEUTRON LAUE CRYSTALLOGRAPHY
1ces CRYSTALS OF DEMETALLIZED CONCANAVALIN A SOAKED WITH ZINC HAVE A ZINC ION BOUND IN THE S1 SITE
1cjp CONCANAVALIN A COMPLEX WITH 4'- METHYLUMBELLIFERYL-ALPHA- D-GLUCOPYRANOSIDE
1cn1 CONCANAVALIN A (DEMETALLIZED)
1con CONCANAVALIN A (CADMIUM SUBSTITUTED FOR MANGANESE)
1cvn CONCANAVALIN A COMPLEXED TO TRIMANNOSIDE
1dq0 LOCKED, METAL-FREE CONCANAVALIN A, A MINOR SPECIES IN SOLUTION
1dq1 CALCIUM;CALCIUM CONCANAVALIN A
1dq2 UNLOCKED METAL-FREE CONCANAVALIN A
1dq4 A TRANSIENT UNLOCKED CONCANAVALIN A STRUCTURE WITH MN2+ BOUND IN THE TRANSITION METAL ION BINDING SITE S1 AND AN EMPTY CALCIUM BINDING SITE S2
1dq5 MANGANESE;MANGANESE CONCANAVALIN A AT PH 5. 0
1dq6 MANGANESE;MANGANESE CONCANAVALIN A AT PH 7. 0
1enq CO-CRYSTALS OF DEMETALLIZED CONCANAVALIN A WITH ZINC HAVING A ZINC ION BOUND IN THE S1 SITE
1enr CO-CRYSTALS OF DEMETALLIZED CONCANAVALIN A WITH ZINC AND CALCIUM HAVING A ZINC ION BOUND IN THE S1 SITE AND A CALCIUM ION BOUND IN THE S2 SITE
1ens CRYSTALS OF DEMETALLIZED CONCANAVALIN A SOAKED WITH COBALT HAVING A COBALT ION BOUND IN THE S1 SITE
1gic CONCANAVALIN A COMPLEXED WITH METHYL ALPHA-D -GLUCOPYRANOSIDE
1gkb CONCANAVALIN A, NEW CRYSTAL FORM
1i3h CONCANAVALIN A-DIMANNOSE STRUCTURE
1jbc CONCANAVALIN A
1jn2 CRYSTAL STRUCTURE OF MESO-TETRASULPHONATOPHENYL PORPHYRINCOMPLEXED WITH CONCANAVALIN A
1joj CONCANAVALIN A-HEXAPEPTIDE COMPLEX
1jui CONCANAVALIN A-CARBOHYDRATE MIMICKING 10-MER PEPTIDE COMPLEX
1jw6 CRYSTAL STRUCTURE OF THE COMPLEX OF CONCANAVALIN A ANDHEXAPEPTIDE
1jyc CONCANAVALIN A/15-MER PEPTIDE COMPLEX
1jyi CONCANAVALIN A/12-MER PEPTIDE COMPLEX
1nls CONCANAVALIN A AND ITS BOUND SOLVENT AT 0 .94A RESOLUTION
1nxd CRYSTAL STRUCTURE OF MNMN CONCANAVALIN A
1ona CO-CRYSTALS OF CONCANAVALIN A WITH METHYL- 3,6-DI-O- (ALPHA-D-MANNOPYRANOSYL)-ALPHA- D-MANNOPYRANOSIDE
1qny X-RAY REFINEMENT OF D2O SOAKED CRYSTAL OF CONCANAVALIN A
1scr CONCANAVALIN A (NICKEL SUBSTITUTED FOR MANGANESE)
1scs CONCANAVALIN A (COBALT SUBSTITUTED FOR MANGANESE)
1tei STRUCTURE OF CONCANAVALIN A COMPLEXED TO BETA-D-GLCNAC (1,2)ALPHA-D-MAN-(1,6)[ BETA-D-GLCNAC(1,2)ALPHA-D-MAN (1,6)] ALPHA-D-MAN
1val CONCANAVALIN A COMPLEX WITH 4'-NITROPHENYL- ALPHA-D- GLUCOPYRANOSIDE
1vam CONCANAVALIN A COMPLEX WITH 4'-NITROPHENYL- ALPHA-D- MANNOPYRANOSIDE
1vln A TRICLINIC CRYSTAL FORM OF THE LECTIN CONCANAVALIN A
1xqn THE 15K NEUTRON STRUCTURE OF SACCHARIDE-FREE CONCANAVALIN A
2cna CONCANAVALIN A
2ctv CONCANAVALIN A (NATIVE)
2enr CO-CRYSTALS OF DEMETALLIZED CONCANAVALIN A WITH CADMIUM HAVING A CADMIUM ION BOUND IN BOTH THE S1 SITE AND THE S2 SITE
3cna CONCANAVALIN A
3enr ZINC-CALCIUM CONCANAVALIN A AT PH 6.15
5cna CONCANAVALIN A COMPLEXED WITH ALPHA-METHYL-D -MANNOPYRANOSIDE