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(-) Description

Title :  METAL-FREE (APO) P. ANGOLENSIS SEED LECTIN IN COMPLEX WITH MAN-ALPHA(1-2)MAN
 
Authors :  A. Garcia-Pino, L. Buts, L. Wyns, R. Loris
Date :  07 Apr 06  (Deposition) - 25 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Legume Lectin, Metal-Free Lectin, Sugar Complex, Man2Man, 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  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1MAN4Ligand/IonALPHA-D-MANNOSE
2PCA2Mod. Amino AcidPYROGLUTAMIC ACID
3SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:13 , SER A:45 , GLY A:104 , GLY A:105 , GLY A:220 , GLU A:221 , MAN A:254 , HOH A:344 , HOH A:345 , HOH A:426BINDING SITE FOR RESIDUE MAN A 253
2AC2SOFTWAREASP A:86 , GLY A:105 , GLY A:106 , PHE A:132 , GLY A:220 , GLU A:221 , GLN A:222 , MAN A:253BINDING SITE FOR RESIDUE MAN A 254
3AC3SOFTWARESER B:45 , GLY B:104 , GLY B:105 , GLY B:220 , MAN B:254 , HOH B:344BINDING SITE FOR RESIDUE MAN B 253
4AC4SOFTWAREASP B:86 , GLY B:105 , GLY B:106 , GLY B:220 , GLU B:221 , GLN B:222 , MAN B:253 , HOH B:371BINDING SITE FOR RESIDUE MAN B 254
5AC5SOFTWAREGLN A:70 , GLN A:72 , SER A:232 , THR A:234BINDING SITE FOR RESIDUE SO4 A 305
6AC6SOFTWAREGLN B:70 , GLN B:72 , SER B:232BINDING SITE FOR RESIDUE SO4 B 306

(-) SS Bonds  (0, 0)

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

(-) 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 2GMM)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GMM)

(-) 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:227
 aligned with Q8GSD2_PTEAG | Q8GSD2 from UniProtKB/TrEMBL  Length:260

    Alignment length:239
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238         
         Q8GSD2_PTEAG     9 QDSLSFGFPTFPSDQKNLIFQGDAQIKNNAVQLTKTDSNGNPVASTVGRILFSAQVHLWEKSSSRVANFQSQFSFSLKSPLSNGADGIAFFIAPPDTTIPSGSGGGLLGLFAPGTAQNTSANQVIAVEFDTFYAQDSNTWDPNYPHIGIDVNSIRSVKTVKWDRRDGQSLNVLVTFNPSTRNLDVVATYSDGTRYEVSYEVDVRSVLPEWVRVGFSAASGEQYQTHTLESWSFTSTLLY 247
               SCOP domains d2gmma_ A: automated matches                                                                                                                                                                                                                    SCOP domains
               CATH domains -2gmmA00 A:2-239  [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.....--------...eeeeee...----........eeeeee..eeeeeeee........eeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeeee.....eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gmm A   1 xDSLSFGFPTFPSDQKNLIFQGDAQIKNNAVQLTKTDSNGNPVASTVGRILFSAQVHLWEKSSSRVANFQSQFSFSLKSPLSNGADGIAFFIAPPDTTIPSGSGGGLLGLFAP--------NQVIAVEFDTFY----NTWDPNYPHIGIDVNSIRSVKTVKWDRRDGQSLNVLVTFNPSTRNLDVVATYSDGTRYEVSYEVDVRSVLPEWVRVGFSAASGEQYQTHTLESWSFTSTLLY 239
                            |       10        20        30        40        50        60        70        80        90       100       110  |      - |     130  |    140       150       160       170       180       190       200       210       220       230         
                            |                                                                                                             113      122        133  138                                                                                                     
                            1-PCA                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:232
 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 d2gmmb_ B: automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains -2gmmB00 B: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.eehhh.eeeeeeeeeeee..........eeeeeee..........hhhhh.....--------...eeeeee...............eeeeee..eeeeeeee.......eeeeeeee.....eeeeeeee....eeeeeee.hhhhh...eeeeeeeeee.......eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gmm B   1 xDSLSFGFPTFPSDQKNLIFQGDAQIKNNAVQLTKTDSNGNPVASTVGRILFSAQVHLWEKSSSRVANFQSQFSFSLKSPLSNGADGIAFFIAPPDTTIPSGSGGGLLGLFAP--------NQVIAVEFDTFYAQDSNTWDPNYPHIGIDVNSIRSVKTVKWDRRDGQSLNVLVTFNPSTRNLDVVATYSDGTRYEVSYEVDVRSVLPEWVRVGFSAASGEQYQTHTLESWSFTSTLLYT 240
                            |       10        20        30        40        50        60        70        80        90       100       110  |      - |     130       140       150       160       170       180       190       200       210       220       230       240
                            1-PCA                                                                                                         113      122
   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 2GMM)

(-) 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
    Ala A:85 - Asp A:86   [ RasMol ]  
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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 2gmp 2gn3 2gn7 2gnb 2gnd 2gnm 2gnt 2phf 2phr 2pht 2phu 2phw 2phx

(-) Related Entries Specified in the PDB File

1ukg 2gme