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(-) Description

Title :  PTEROCARPUS ANGOLENSIS LECTIN (PAL) IN COMPLEX WITH MAN-9
 
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 :  1.80
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, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA2Ligand/IonCALCIUM ION
3MAN8Ligand/IonALPHA-D-MANNOSE
4MN2Ligand/IonMANGANESE (II) ION
5PCA2Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:85 , ASP A:86 , GLY A:105 , GLY A:106 , PHE A:132 , ASN A:138 , GLY A:220 , GLU A:221 , GLN A:222 , MAN A:254 , HOH A:403 , HOH A:451BINDING SITE FOR RESIDUE MAN A 253
02AC2SOFTWAREASN A:68 , PHE A:132 , ASP A:136 , SER A:137 , THR A:175 , ASN A:177 , GLU A:221 , GLN A:222 , MAN A:253 , HOH A:406BINDING SITE FOR RESIDUE MAN A 254
03AC3SOFTWARESER B:45 , GLY B:104 , GLY B:105 , GLU B:221 , MAN B:254 , HOH B:377 , HOH B:438 , HOH B:494BINDING SITE FOR RESIDUE MAN B 253
04AC4SOFTWAREALA 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:445BINDING SITE FOR RESIDUE MAN B 254
05AC5SOFTWAREPHE 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:258 , HOH B:456BINDING SITE FOR RESIDUE MAN B 255
06AC6SOFTWAREASN B:83 , ASP B:136 , MAN B:255 , MAN B:257BINDING SITE FOR RESIDUE MAN B 256
07AC7SOFTWAREMAN B:256BINDING SITE FOR RESIDUE MAN B 257
08AC8SOFTWAREASP B:136 , GLU B:221 , MAN B:255 , MAN B:259BINDING SITE FOR RESIDUE BMA B 258
09AC9SOFTWAREBMA B:258 , HOH B:466BINDING SITE FOR RESIDUE MAN B 259
10BC1SOFTWAREGLU B:128 , ASP B:130 , ASP B:141 , HIS B:146 , HOH B:305 , HOH B:306BINDING SITE FOR RESIDUE MN B 301
11BC2SOFTWAREASP B:130 , PHE B:132 , ASN B:138 , ASP B:141 , HOH B:303 , HOH B:304BINDING SITE FOR RESIDUE CA B 302
12BC3SOFTWAREGLU A:128 , ASP A:130 , ASP A:141 , HIS A:146 , HOH A:305 , HOH A:306BINDING SITE FOR RESIDUE MN A 301
13BC4SOFTWAREASP A:130 , PHE A:132 , ASN A:138 , ASP A:141 , HOH A:303 , HOH A:304BINDING SITE FOR RESIDUE CA A 302

(-) SS Bonds  (0, 0)

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

(-) 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 2PHW)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PHW)

(-) 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:240
 aligned with Q8GSD2_PTEAG | Q8GSD2 from UniProtKB/TrEMBL  Length:260

    Alignment length:240
                                    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 QDSLSFGFPTFPSDQKNLIFQGDAQIKNNAVQLTKTDSNGNPVASTVGRILFSAQVHLWEKSSSRVANFQSQFSFSLKSPLSNGADGIAFFIAPPDTTIPSGSGGGLLGLFAPGTAQNTSANQVIAVEFDTFYAQDSNTWDPNYPHIGIDVNSIRSVKTVKWDRRDGQSLNVLVTFNPSTRNLDVVATYSDGTRYEVSYEVDVRSVLPEWVRVGFSAASGEQYQTHTLESWSFTSTLLYT 248
               SCOP domains d2phwa_ A: automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains -2phwA00 A:2-240  [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........eeeeee...............eeeeee......eeee........eeeeeeee....eeeeeeee....eeeeeee.hhhhh...eeeeeeeeee.....eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2phw A   1 xDSLSFGFPTFPSDQKNLIFQGDAQIKNNAVQLTKTDSNGNPVASTVGRILFSAQVHLWEKSSSRVANFQSQFSFSLKSPLSNGADGIAFFIAPPDTTIPSGSGGGLLGLFAPGTAQNTSANQVIAVEFDTFYAQDSNTWDPNYPHIGIDVNSIRSVKTVKWDRRDGQSLNVLVTFNPSTRNLDVVATYSDGTRYEVSYEVDVRSVLPEWVRVGFSAASGEQYQTHTLESWSFTSTLLYT 240
                            |       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:240
 aligned with Q8GSD2_PTEAG | Q8GSD2 from UniProtKB/TrEMBL  Length:260

    Alignment length:240
                                    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 QDSLSFGFPTFPSDQKNLIFQGDAQIKNNAVQLTKTDSNGNPVASTVGRILFSAQVHLWEKSSSRVANFQSQFSFSLKSPLSNGADGIAFFIAPPDTTIPSGSGGGLLGLFAPGTAQNTSANQVIAVEFDTFYAQDSNTWDPNYPHIGIDVNSIRSVKTVKWDRRDGQSLNVLVTFNPSTRNLDVVATYSDGTRYEVSYEVDVRSVLPEWVRVGFSAASGEQYQTHTLESWSFTSTLLYT 248
               SCOP domains d2phwb_ B: automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains -2phwB00 B:2-240  [code=2.60.120.200, no name defined]                                                                                                                                                                                           CATH domains
           Pfam domains (1) -Lectin_legB-2phwB01 B:2-234                                                                                                                                                                                                              ------ Pfam domains (1)
           Pfam domains (2) -Lectin_legB-2phwB02 B:2-234                                                                                                                                                                                                              ------ Pfam domains (2)
         Sec.struct. author ..eeeeee.........eeeee..eee..eee.............eeeeeee...ee.ee....eeeeeeeeeeeeee........eeeeeee..........hhhhh...hhhhh........eeeeee...............eeeeee......eeee........eeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeeee.....eeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2phw B   1 xDSLSFGFPTFPSDQKNLIFQGDAQIKNNAVQLTKTDSNGNPVASTVGRILFSAQVHLWEKSSSRVANFQSQFSFSLKSPLSNGADGIAFFIAPPDTTIPSGSGGGLLGLFAPGTAQNTSANQVIAVEFDTFYAQDSNTWDPNYPHIGIDVNSIRSVKTVKWDRRDGQSLNVLVTFNPSTRNLDVVATYSDGTRYEVSYEVDVRSVLPEWVRVGFSAASGEQYQTHTLESWSFTSTLLYT 240
                            |       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.

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  Cis Peptide Bonds
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 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 2pht 2phu 2phx

(-) Related Entries Specified in the PDB File

1q8p 2phf 2phr 2pht 2phu 2phx