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(-) Description

Title :  CYANIDE BINDING AND HEME CAVITY CONFORMATIONAL TRANSITIONS IN DROSOPHILA MELANOGASTER HEXA-COORDINATE HEMOGLOBIN
 
Authors :  D. De Sanctis, P. Ascenzi, A. Bocedi, S. Dewilde, T. Burmester, T. Hankeln, L. Moens, M. Bolognesi
Date :  20 Feb 06  (Deposition) - 03 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Drosophila Melanogaster Hemoglobin Structure; Hexa- Coordinate Hemoglobin; Cyanide Binding To Hemoglobin; Heme Distal Site Structure; Fruit Fly Hemoglobin, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. De Sanctis, P. Ascenzi, A. Bocedi, S. Dewilde, T. Burmester, T. Hankeln, L. Moens, M. Bolognesi
Cyanide Binding And Heme Cavity Conformational Transitions In Drosophila Melanogaster Hexacoordinate Hemoglobin.
Biochemistry V. 45 10054 2006
PubMed-ID: 16906763  |  Reference-DOI: 10.1021/BI060462A
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLOBIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GLOB1
    Mutation: YES
    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  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2CYN1Ligand/IonCYANIDE ION
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4MG1Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:35 , PRO A:36 , SER A:37BINDING SITE FOR RESIDUE CL A 161
2AC2SOFTWARETHR A:19 , PRO A:20 , THR A:21 , ASP A:22 , HOH A:5081BINDING SITE FOR RESIDUE CL A 163
3AC3SOFTWAREGLU A:14 , HOH A:5011 , HOH A:5012 , HOH A:5013 , HOH A:5014 , HOH A:5015BINDING SITE FOR RESIDUE MG A 162
4AC4SOFTWAREHIS A:61 , ILE A:65 , HEM A:154BINDING SITE FOR RESIDUE CYN A 1802
5AC5SOFTWAREASN A:38 , LYS A:41 , PHE A:42 , PRO A:43 , ARG A:57 , HIS A:61 , VAL A:68 , TRP A:89 , SER A:95 , HIS A:96 , ARG A:99 , VAL A:101 , SER A:105 , TYR A:106 , LEU A:109 , CYN A:1802 , HOH A:5016 , HOH A:5019 , HOH A:5061 , HOH A:5206 , HOH A:5233BINDING SITE FOR RESIDUE HEM A 154

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2G3H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2G3H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2G3H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2G3H)

(-) Exons   (0, 0)

(no "Exon" information available for 2G3H)

(-) 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:153
 aligned with Q9VF15_DROME | Q9VF15 from UniProtKB/TrEMBL  Length:153

    Alignment length:153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   
         Q9VF15_DROME     1 MNSDEVQLIKKTWEIPVATPTDSGAAILTQFFNRFPSNLEKFPFRDVPLEELSGNARFRAHAGRIIRVFDESIQVLGQDGDLEKLDEIWTKIAVSHIPRTVSKESYNQLKGVILDVLTAACSLDESQAATWAKLVDHVYGIIFKAIDDDGNAK 153
               SCOP domains d2g3ha_ A: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g3h A   1 MNSDEVQLIKKTWEIPVATPTDSGAAILTQFFNRFPSNLEKFPFRDVPLEELSGNARFRAHAGRIIRVFDESIQVLGQDGDLEKLDEIWTKIAVSHIPRTVSKESYNQLKGVILDVLTAASSLDESQAATWAKLVDHVYGIIFKAIDDDGNAK 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2G3H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G3H)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9VF15_DROME | Q9VF15)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0019825    oxygen binding    Interacting selectively and non-covalently with oxygen (O2).
    GO:0005344    oxygen transporter activity    Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
    GO:0015671    oxygen transport    The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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        Q9VF15_DROME | Q9VF15: 2bk9

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