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(-) Description

Title :  CRYSTAL STRUCTURE OF CARBONMONOXY HEMOGLOBIN D FROM THE ALDABRA GIANT TORTOISE, GEOCHELONE GIGANTEA
 
Authors :  T. Kuwada, T. Hasegawa, I. Sato, K. Ishikawa, F. Shishikura
Date :  04 Aug 07  (Deposition) - 28 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Hemoglobin D, Reptilia, The Aldabra Giant Tortoise, Geochelone Gigantea, Heme, Iron, Metal-Binding, Oxygen Transport, Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Kuwada, T. Hasegawa, I Sato, K. Ishikawa, F. Shishikura
Crystal Structure Of The Ligated Hemoglobin D From The Aldabra Giant Tortoise, Geochelone Gigantea
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOGLOBIN D SUBUNIT ALPHA
    Chains: A
    Organism Common: ALDABRA GIANT TORTOISE
    Organism Scientific: DIPSOCHELYS DUSSUMIERI
    Organism Taxid: 167804
    Synonym: HEMOGLOBIN D ALPHA CHAIN
    Tissue: RED BLOOD CELL
 
Molecule 2 - HEMOGLOBIN A/D SUBUNIT BETA
    Chains: B
    Organism Common: ALDABRA GIANT TORTOISE
    Organism Scientific: DIPSOCHELYS DUSSUMIERI
    Organism Taxid: 167804
    Synonym: HEMOGLOBIN A/D BETA CHAIN
    Tissue: RED BLOOD CELL

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CMO2Ligand/IonCARBON MONOXIDE
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CMO4Ligand/IonCARBON MONOXIDE
2HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:42 , PHE A:43 , HIS A:45 , PHE A:46 , HIS A:58 , ALA A:65 , LEU A:83 , HIS A:87 , LEU A:91 , VAL A:93 , ASN A:97 , PHE A:98 , LEU A:101 , LEU A:136 , CMO A:151 , HOH A:160 , HOH A:162 , HOH A:237 , HOH A:274 , HOH B:172 , HOH B:185BINDING SITE FOR RESIDUE HEM A 150
2AC2SOFTWAREHIS A:58 , VAL A:62 , HEM A:150BINDING SITE FOR RESIDUE CMO A 151
3AC3SOFTWARETHR B:38 , PHE B:41 , PHE B:42 , PHE B:45 , LYS B:59 , HIS B:63 , LYS B:66 , SER B:70 , LEU B:88 , HIS B:92 , LEU B:96 , VAL B:98 , ASN B:102 , PHE B:103 , LEU B:106 , LEU B:141 , CMO B:151 , HOH B:225 , HOH B:229 , HOH B:272 , HOH B:317 , HOH B:367BINDING SITE FOR RESIDUE HEM B 150
4AC4SOFTWAREHIS B:63 , VAL B:67 , HEM B:150BINDING SITE FOR RESIDUE CMO B 151

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z6N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z6N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z6N)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBAD_ALDGI2-141  1A:2-141
HBB_ALDGI4-146  1B:4-146
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBAD_ALDGI2-141  2A:2-141
HBB_ALDGI4-146  2B:4-146

(-) Exons   (0, 0)

(no "Exon" information available for 2Z6N)

(-) Sequences/Alignments

Asymmetric 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:141
 aligned with HBAD_ALDGI | P83134 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 
           HBAD_ALDGI     1 MLTEDDKQLIQHVWEKVLEHQEDFGAEALERMFIVYPSTKTYFPHFDLHHDSEQIRHHGKKVVGALGDAVKHIDNLSATLSELSNLHAYNLRVDPVNFKLLSHCFQVVLGAHLGREYTPQVQVAYDKFLAAVSAVLAEKYR 141
               SCOP domains d2z6na_ A: Hemoglobin, alpha-chain                                                                                                            SCOP domains
               CATH domains 2z6nA00 A:1-141 Globins                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: A:2-141 UniProt: 2-141                                                                                                          PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z6n A   1 MLTEDDKQLIQHVWEKVLEHQEDFGAEALERMFIVYPSTKTYFPHFDLHHDSEQIRHHGKKVVGALGDAVKHIDNLSATLSELSNLHAYNLRVDPVNFKLLSHCFQVVLGAHLGREYTPQVQVAYDKFLAAVSAVLAEKYR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 


Chain B from PDB  Type:PROTEIN  Length:146
 aligned with HBB_ALDGI | P83133 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
            HBB_ALDGI     1 VHWTSEEKQYITSLWAKVNVGEVGGEALARLLIVYPWTQRFFASFGNLSSANAILHNAKVLAHGQKVLTSFGEAVKNLDNIKKTFAQLSELHCEKLHVDPENFKLLGNILIIVLATHFPKEFTPASQAAWTKLVNAVAHALALGYH 146
               SCOP domains d2z6nb_ B: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 2z6nB00 B:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---GLOBIN  PDB: B:4-146 UniProt: 4-146                                                                                                             PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z6n B   1 VHWTSEEKQYITSLWAKVNVGEVGGEALARLLIVYPWTQRFFASFGNLSSANAILHNAKVLAHGQKVLTSFGEAVKNLDNIKKTFAQLSELHCEKLHVDPENFKLLGNILIIVLATHFPKEFTPASQAAWTKLVNAVAHALALGYH 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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  (2, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Z6N)

(-) Gene Ontology  (8, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (HBAD_ALDGI | P83134)
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:0005833    hemoglobin complex    An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.

Chain B   (HBB_ALDGI | P83133)
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:0005833    hemoglobin complex    An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HBAD_ALDGI | P83134: 1v75 1wmu
        HBB_ALDGI | P83133: 1v75 1wmu

(-) Related Entries Specified in the PDB File

1v75 THE SAME HEMOGLOBIN COMPONENT IN THE AQUOMET FORM
1wmu THE SAME HEMOGLOBIN COMPONENT IN THE AQUOMET FORM