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(-) Description

Title :  P. ANGOLENSIS LECTIN (PAL) TREATED WITH EDTA FOR 39 HOURS
 
Authors :  A. Garcia-Pino, L. Buts, L. Wyns, R. Loris
Date :  10 Apr 06  (Deposition) - 25 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Legume Lectin, Metal-Free Lectin, Edta Treatment, Pal, Sugar Complex, Mannose, Beta Sandwich, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Garcia-Pino, L. Buts, L. Wyns, R. Loris
Interplay Between Metal Binding And Cis/Trans Isomerization In Legume Lectins: Structural And Thermodynamic Study Of P. Angolensis Lectin.
J. Mol. Biol. V. 361 153 2006
PubMed-ID: 16824540  |  Reference-DOI: 10.1016/J.JMB.2006.06.006
(for further references see the PDB file header)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MAN1Ligand/IonALPHA-D-MANNOSE
3MN2Ligand/IonMANGANESE (II) ION
4PCA2Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:85 , ASP A:86 , GLY A:105 , GLY A:106 , PHE A:132 , SER A:137 , GLY A:220 , GLU A:221 , GLN A:222 , HOH A:309BINDING SITE FOR RESIDUE MAN A 253
2AC2SOFTWAREGLU A:128 , ASP A:130 , HIS A:146 , HOH A:257 , HOH A:258 , HOH A:336BINDING SITE FOR RESIDUE CA A 254
3AC3SOFTWAREASP A:130 , HOH A:321BINDING SITE FOR RESIDUE MN A 255
4AC4SOFTWAREGLU B:128 , ASP B:130 , HIS B:146 , HOH B:267 , HOH B:268BINDING SITE FOR RESIDUE CA B 253
5AC5SOFTWAREASP B:130 , PHE B:132 , HOH B:266BINDING SITE FOR RESIDUE MN B 254

(-) SS Bonds  (0, 0)

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

(-) 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 2GNM)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GNM)

(-) 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 d2gnma_ A: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains -2gnmA00 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..eeeeee...............eeeeee......eeee........eeeeeeee....eeeeeeee....eeeeeee.hhhhh...eeeeeeeeee.....eeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gnm 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:240
 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 d2gnmb_ B: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains -2gnmB00 B: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........eeeeee..-............eeeeee......eeee........eeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeeee.....eeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gnm B   1 xDSLSFGFPTFPSDQKNLIFQGDAQIKNNAVQLTKTDSNGNPVASTVGRILFSAQVHLWEKSSSRVANFQSQFSFSLKSPLSNGADGIAFFIAPPDTTIPSGSGGGLLGLFAPGTAQNTSANQVIAVEFDTF-AQDSNTWDPNYPHIGIDVNSIRSVKTVKWDRRDGQSLNVLVTFNPSTRNLDVVATYSDGTRYEVSYEVDVRSVLPEWVRVGFSAASGEQYQTHTLESWSFTSTLLYTA 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                                                                                                                            132 |                                                                                                           
                                                                                                                                                               134
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "Pfam Domain" information available for 2GNM)

(-) 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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 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 2gnt 2phf 2phr 2pht 2phu 2phw 2phx

(-) Related Entries Specified in the PDB File

1ukg 2gme 2gmm 2gmp 2gn3 2gnb 2gnd 2gnt