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

(-) Description

Title :  PTEROCARPUS ANGOLENSIS LECTIN (P L) IN COMPLEX WITH MAN-7D3
 
Authors :  A. Garcia-Pino, L. Buts, L. Wyns, A. Imberty, R. Loris
Date :  12 Apr 07  (Deposition) - 10 Jul 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lectin, Carbohydrate, High Mannose, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Garcia-Pino, L. Buts, L. Wyns, A. Imberty, R. Loris
How A Plant Lectin Recognizes High Mannose Oligosaccharides
Plant Physiol. V. 144 1733 2007
PubMed-ID: 17556509  |  Reference-DOI: 10.1104/PP.107.100867
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LECTIN
    Chains: A, B
    Organism Scientific: PTEROCARPUS ANGOLENSIS
    Organism Taxid: 182271

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 14)

Asymmetric/Biological Unit (5, 14)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA2Ligand/IonCALCIUM ION
3MAN7Ligand/IonALPHA-D-MANNOSE
4MN2Ligand/IonMANGANESE (II) ION
5PCA2Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:45 , GLY A:104 , GLY A:105 , GLY A:220 , MAN A:254 , HOH A:335 , HOH A:370BINDING SITE FOR RESIDUE MAN A 253
02AC2SOFTWAREALA A:85 , ASP A:86 , GLY A:106 , PHE A:132 , ASN A:138 , GLY A:220 , GLU A:221 , GLN A:222 , MAN A:253 , MAN A:255BINDING SITE FOR RESIDUE MAN A 254
03AC3SOFTWAREMAN A:254BINDING SITE FOR RESIDUE MAN A 255
04AC4SOFTWARESER B:45 , GLY B:104 , GLY B:105 , GLU B:221 , MAN B:254 , HOH B:362 , HOH B:384BINDING SITE FOR RESIDUE MAN B 253
05AC5SOFTWAREALA B:85 , ASP B:86 , GLY B:106 , PHE B:132 , ASN B:138 , GLY B:220 , GLU B:221 , GLN B:222 , MAN B:253 , MAN B:255 , HOH B:370BINDING SITE FOR RESIDUE MAN B 254
06AC6SOFTWAREPHE B:132 , ALA B:134 , ASP B:136 , SER B:137 , GLU B:221 , GLN B:222 , MAN B:254 , MAN B:256 , BMA B:257 , HOH B:399BINDING SITE FOR RESIDUE MAN B 255
07AC7SOFTWAREASN B:83 , ASP B:136 , MAN B:255BINDING SITE FOR RESIDUE MAN B 256
08AC8SOFTWAREASP B:136 , MAN B:255 , HOH B:387BINDING SITE FOR RESIDUE BMA B 257
09AC9SOFTWAREGLU A:128 , ASP A:130 , ASP A:141 , HIS A:146 , HOH A:304 , HOH A:305BINDING SITE FOR RESIDUE MN A 301
10BC1SOFTWAREASP A:130 , PHE A:132 , ASN A:138 , ASP A:141 , HOH A:303 , HOH A:306BINDING SITE FOR RESIDUE CA A 302
11BC2SOFTWAREGLU B:128 , ASP B:130 , ASP B:141 , HIS B:146 , HOH B:303 , HOH B:304BINDING SITE FOR RESIDUE MN B 301
12BC3SOFTWAREASP B:130 , PHE B:132 , ASN B:138 , ASP B:141 , HOH B:305 , HOH B:308BINDING SITE FOR RESIDUE CA B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:85 -Asp A:86
2Ala B:85 -Asp B:86

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PHT)

(-) 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:241
 aligned with Q8GSD2_PTEAG | Q8GSD2 from UniProtKB/TrEMBL  Length:260

    Alignment length:241
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248 
         Q8GSD2_PTEAG     9 QDSLSFGFPTFPSDQKNLIFQGDAQIKNNAVQLTKTDSNGNPVASTVGRILFSAQVHLWEKSSSRVANFQSQFSFSLKSPLSNGADGIAFFIAPPDTTIPSGSGGGLLGLFAPGTAQNTSANQVIAVEFDTFYAQDSNTWDPNYPHIGIDVNSIRSVKTVKWDRRDGQSLNVLVTFNPSTRNLDVVATYSDGTRYEVSYEVDVRSVLPEWVRVGFSAASGEQYQTHTLESWSFTSTLLYTA 249
               SCOP domains d2phta_ A: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains -2phtA00 A:2-241  [code=2.60.120.200, no name defined]                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........eeeee..eee..eee.............eeeeeee...ee.ee....eeeeeeeeeeeeee........eeeeeee..........hhhhh...hhhhh.hhhhh..eeeeee...............eeeeee......eeee........eeeeeeee....eeeeeeee....eeeeeee.hhhhh...eeeeeeeeee.....eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pht A   1 xDSLSFGFPTFPSDQKNLIFQGDAQIKNNAVQLTKTDSNGNPVASTVGRILFSAQVHLWEKSSSRVANFQSQFSFSLKSPLSNGADGIAFFIAPPDTTIPSGSGGGLLGLFAPGTAQNTSANQVIAVEFDTFYAQDSNTWDPNYPHIGIDVNSIRSVKTVKWDRRDGQSLNVLVTFNPSTRNLDVVATYSDGTRYEVSYEVDVRSVLPEWVRVGFSAASGEQYQTHTLESWSFTSTLLYTA 241
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 
                            |                                                                                                                                                                                                                                                
                            1-PCA                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:241
 aligned with Q8GSD2_PTEAG | Q8GSD2 from UniProtKB/TrEMBL  Length:260

    Alignment length:241
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248 
         Q8GSD2_PTEAG     9 QDSLSFGFPTFPSDQKNLIFQGDAQIKNNAVQLTKTDSNGNPVASTVGRILFSAQVHLWEKSSSRVANFQSQFSFSLKSPLSNGADGIAFFIAPPDTTIPSGSGGGLLGLFAPGTAQNTSANQVIAVEFDTFYAQDSNTWDPNYPHIGIDVNSIRSVKTVKWDRRDGQSLNVLVTFNPSTRNLDVVATYSDGTRYEVSYEVDVRSVLPEWVRVGFSAASGEQYQTHTLESWSFTSTLLYTA 249
               SCOP domains d2phtb_ B: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains -2phtB00 B:2-241  [code=2.60.120.200, no name defined]                                                                                                                                                                                            CATH domains
           Pfam domains (1) -Lectin_legB-2phtB01 B:2-234                                                                                                                                                                                                              ------- Pfam domains (1)
           Pfam domains (2) -Lectin_legB-2phtB02 B:2-234                                                                                                                                                                                                              ------- Pfam domains (2)
         Sec.struct. author ..eeeeee.........eeeee..eee..eee.............eeeeeee...ee.ee....eeeeeeeeeeeeee........eeeeeee..........hhhhh................eeeeee...............eeeeee......eeee........eeeeeeee....eeeeeeee....eeeeeee.hhhhh...eeeeeeeeee.....eeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pht B   1 xDSLSFGFPTFPSDQKNLIFQGDAQIKNNAVQLTKTDSNGNPVASTVGRILFSAQVHLWEKSSSRVANFQSQFSFSLKSPLSNGADGIAFFIAPPDTTIPSGSGGGLLGLFAPGTAQNTSANQVIAVEFDTFYAQDSNTWDPNYPHIGIDVNSIRSVKTVKWDRRDGQSLNVLVTFNPSTRNLDVVATYSDGTRYEVSYEVDVRSVLPEWVRVGFSAASGEQYQTHTLESWSFTSTLLYTA 241
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 
                            1-PCA
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Concanavalin (293)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8GSD2_PTEAG | Q8GSD2)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    BMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PCA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:85 - Asp A:86   [ RasMol ]  
    Ala B:85 - Asp B:86   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  2pht
    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
  Q8GSD2_PTEAG | Q8GSD2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q8GSD2_PTEAG | Q8GSD2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8GSD2_PTEAG | Q8GSD2: 1n3o 1n3p 1n3q 1q8o 1q8p 1q8q 1q8s 1q8v 1s1a 1ukg 2ar6 2arb 2are 2arx 2auy 2gme 2gmm 2gmp 2gn3 2gn7 2gnb 2gnd 2gnm 2gnt 2phf 2phr 2phu 2phw 2phx

(-) Related Entries Specified in the PDB File

1q8p PTEROCARPUS ANGOLENSIS LECTIN COMPLEXED WITH MAN(A1-3)MAN
2phf
2phr
2phu
2phw
2phx