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(-) Description

Title :  CRYSTAL STRUCTURE OF IMAGINAL DISC GROWTH FACTOR-2
 
Authors :  P. F. Varela, A. S. Llera, R. A. Mariuzza, J. Tormo
Date :  23 Jul 01  (Deposition) - 01 May 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Idgf, Imaginal Disc, Growth Factor, Chitinase, Insulin Receptor, Heparin, Hormone-Growth Factor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. F. Varela, A. S. Llera, R. A. Mariuzza, J. Tormo
Crystal Structure Of Imaginal Disc Growth Factor-2. A Membe Of A New Family Of Growth-Promoting Glycoproteins From Drosophila Melanogaster.
J. Biol. Chem. V. 277 13229 2002
PubMed-ID: 11821393  |  Reference-DOI: 10.1074/JBC.M110502200

(-) Compounds

Molecule 1 - IMAGINAL DISC GROWTH FACTOR-2
    Chains: A
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN1Ligand/IonALPHA-D-MANNOSE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:136 , ASN A:200 , THR A:202 , HIS A:252 , PHE A:257 , GLN A:258 , HOH A:1065 , HOH A:1066 , HOH A:1108 , HOH A:1267 , HOH A:1289 , HOH A:1376 , NAG A:3101BINDING SITE FOR RESIDUE NAG A 3100
2AC2SOFTWAREPHE A:257 , HOH A:1267 , HOH A:1274 , HOH A:1277 , HOH A:1368 , HOH A:1493 , HOH A:1632 , NAG A:3100 , BMA A:3102BINDING SITE FOR RESIDUE NAG A 3101
3AC3SOFTWAREALA A:251 , HOH A:1226 , HOH A:1490 , HOH A:1697 , NAG A:3101 , MAN A:3103BINDING SITE FOR RESIDUE BMA A 3102
4AC4SOFTWAREHOH A:1532 , HOH A:1642 , BMA A:3102BINDING SITE FOR RESIDUE MAN A 3103

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:6 -A:33
2A:322 -A:405

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:39 -Tyr A:40
2Pro A:295 -Val A:296
3Phe A:394 -Asp A:395

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JND)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JND)

(-) Exons   (0, 0)

(no "Exon" information available for 1JND)

(-) 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:400
 aligned with IDGF2_DROME | Q9V3D4 from UniProtKB/Swiss-Prot  Length:440

    Alignment length:419
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431         
          IDGF2_DROME    22 SNLVCYYDSSSYTREGLGKLLNPDLEIALQFCSHLVYGYAGLRGENLQAYSMNENLDIYKHQFSEVTSLKRKYPHLKVLLSVGGDHDIDPDHPNKYIDLLEGEKVRQIGFIRSAYDLVKTYGFDGLDLAYQFPKNKPRKVHGDLGLAWKSIKKLFTGDFIVDPHAALHKEQFTALVRDVKDSLRADGFLLSLTVLPNVNSTWYFDIPALNGLVDFVNLATFDFLTPARNPEEADYSAPIYHPDGSKDRLAHLNADFQVEYWLSQGFPSNKINLGVATYGNAWKLTKDSGLEGVPVVPETSGPAPEGFQSQKPGLLSYAEICGKLSNPQNQFLKGNESPLRRVSDPTKRFGGIAYRPVDGQITEGIWVSYDDPDSASNKAAYARVKNLGGVALFDLSYDDFRGQCSGDKYPILRAIKYRL 440
               SCOP domains d1jnda1 A:2-278,A:371-420 Imaginal disc growth factor-2                                                                                                                                                                                                                              d1jnda2 A:279-370 Imaginal disc growth factor-2                                             d1jnda1 A:2-278,A:371-420                          SCOP domains
               CATH domains 1jndA01 A:2-277,A:372-420 Glycosidases                                                                                                                                                                                                                                              1jndA02 A:278-371  [code=3.10.50.10, no name defined]                                         1jndA01 A:2-277,A:372-420 Glycosidases            CATH domains
               Pfam domains Glyco_hydro_18-1jndA01 A:2-399                                                                                                                                                                                                                                                                                                                                                                                --------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhh......hhhhhhhhhhhh.eeeeeeeee......eee.hhhhhh..hhhhhhhhhhhh....eeeeeee..........hhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeeee...........-------------------....hhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhh...eeee..................................hhhhhhhhhhhh..hhh.eeeeee.eeeeee.hhhhh........................eeehhhhhhhh........hhhhh..eee........eeeee.........eeeee.hhhhhhhhhhhhhhh...eeeeehhhhh..........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jnd A   2 SNLVCYYDSSSYTREGLGKLLNPDLEIALQFCSHLVYGYAGLRGENLQAYSMNENLDIYKHQFSEVTSLKRKYPHLKVLLSVGGDHDIDPDHPNKYIDLLEGEKVRQIGFIRSAYELVKTYGFDGLDLAYQFPKNKPRKV-------------------IVDPHAALHKEQFTALVRDVKDSLRADGFLLSLTVLPNVNSTWYFDIPALNGLVDFVNLATFDFLTPARNPEEADYSAPIYHPDGSKDRLAHLNADFQVEYWLSQGFPSNKINLGVATYGNAWKLTKDSGLEGVPVVPETSGPAPEGFQSQKPGLLSYAEICGKLSNPQNQFLKGNESPLRRVSDPTKRFGGIAYRPVDGQITEGIWVSYDDPDSASNKAAYARVKNLGGVALFDLSYDDFRGQCSGDKYPILRAIKYRL 420
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         -       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411         
                                                                                                                                                                     141                 161
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IDGF2_DROME | Q9V3D4)
molecular function
    GO:0008061    chitin binding    Interacting selectively and non-covalently with chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    GO:0004568    chitinase activity    Catalysis of the hydrolysis of (1->4)-beta linkages of N-acetyl-D-glucosamine (GlcNAc) polymers of chitin and chitodextrins.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0008084    imaginal disc growth factor receptor binding    Interacting selectively and non-covalently with an imaginal disc growth factor receptor.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006032    chitin catabolic process    The chemical reactions and pathways resulting in the breakdown of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    GO:0007444    imaginal disc development    The process whose specific outcome is the progression of the imaginal disc over time, from its formation to the metamorphosis to form adult structures. Imaginal discs are epithelial infoldings in the larvae of holometabolous insects that develop into adult structures (legs, antennae, wings, etc.).
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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        IDGF2_DROME | Q9V3D4: 1jne

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