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(-) Description

Title :  R-STATE FORM OF CHICKEN HEMOGLOBIN D
 
Authors :  E. Knapp, M. A. Oliveira, Q. Xie, S. R. Ernst, A. F. Riggs, M. L. Hackert
Date :  06 Dec 98  (Deposition) - 26 Mar 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hemoglobin D (R-State) 1, Hemoglobin, Avian, High Cooperatiity, Oxygen Transport, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. Knapp, M. A. Oliveira, Q. Xie, S. R. Ernst, A. F. Riggs, M. L. Hackert
The Structural And Functional Analysis Of The Hemoglobin D Component From Chicken.
J. Biol. Chem. V. 274 6411 1999
PubMed-ID: 10037733  |  Reference-DOI: 10.1074/JBC.274.10.6411
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (HEMOGLOBIN D)
    Cell: ERYTHROCYTES
    Cellular Location: CYTOPLASM
    Chains: A, C
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
    Synonym: HB D
    Tissue: BLOOD
 
Molecule 2 - PROTEIN (HEMOGLOBIN D)
    Cell: ERYTHROCYTES
    Cellular Location: CYTOPLASM
    Chains: B, D
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
    Synonym: HB D
    Tissue: BLOOD

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1HEM4Ligand/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 , LYS A:61 , LEU A:83 , HIS A:87 , LEU A:91 , VAL A:93 , ASN A:97 , PHE A:98 , LEU A:101 , HOH A:143 , HOH A:144 , HOH A:156BINDING SITE FOR RESIDUE HEM A 142
2AC2SOFTWARETHR B:38 , PHE B:41 , PHE B:42 , HIS B:63 , LYS B:66 , SER B:70 , LEU B:88 , HIS B:92 , VAL B:98 , ASN B:102 , LEU B:106 , LEU B:141 , HOH B:148 , HOH B:149 , HOH B:165BINDING SITE FOR RESIDUE HEM B 147
3AC3SOFTWARETYR C:42 , PHE C:43 , HIS C:45 , PHE C:46 , HIS C:58 , LEU C:83 , HIS C:87 , LEU C:91 , VAL C:93 , ASN C:97 , PHE C:98 , LEU C:101 , HOH C:145 , HOH C:172BINDING SITE FOR RESIDUE HEM C 142
4AC4SOFTWAREPHE D:41 , PHE D:42 , HIS D:63 , LYS D:66 , LEU D:88 , HIS D:92 , LEU D:96 , VAL D:98 , ASN D:102 , PHE D:103 , LEU D:106 , LEU D:141 , HOH D:148 , HOH D:149BINDING SITE FOR RESIDUE HEM D 147

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HBR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HBR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_HBB_CHICK_001 *T70SHBB_CHICK  ---  ---B/DT69S
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBAD_CHICK2-141
 		  2A:2-141
C:2-141
HBB_CHICK5-147
 		  2B:4-144
D:4-146

(-) Exons   (0, 0)

(no "Exon" information available for 1HBR)

(-) 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:141
 aligned with HBAD_CHICK | P02001 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 
           HBAD_CHICK     1 MLTAEDKKLIQQAWEKAASHQEEFGAEALTRMFTTYPQTKTYFPHFDLSPGSDQVRGHGKKVLGALGNAVKNVDNLSQAMAELSNLHAYNLRVDPVNFKLLSQCIQVVLAVHMGKDYTPEVHAAFDKFLSAVSAVLAEKYR 141
               SCOP domains d1hbra_ A: Hemoglobin, alpha-chain                                                                                                            SCOP domains
               CATH domains 1hbrA00 A:1-141 Globins                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhh..........hhhhhhhhhhhhhhhhhhh....hhhh.hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: A:2-141 UniProt: 2-141                                                                                                          PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hbr A   1 MLTAEDKKLIQQAWEKAASHQEEFGAEALTRMFTTYPQTKTYFPHFDLSPGSDQVRGHGKKVLGALGNAVKNVDNLSQAMAELSNLHAYNLRVDPVNFKLLSQCIQVVLAVHMGKDYTPEVHAAFDKFLSAVSAVLAEKYR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 


Chain B from PDB  Type:PROTEIN  Length:144
 aligned with HBB_CHICK | P02112 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:144
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141    
            HBB_CHICK     2 VHWTAEEKQLITGLWGKVNVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPMVRAHGKKVLTSFGDAVKNLDNIKNTFSQLSELHCDKLHVDPENFRLLGDILIIVLAAHFSKDFTPECQAAWQKLVRVVAHALARK 145
               SCOP domains d1hbrb_ B: Hemoglobin, beta-chain                                                                                                                SCOP domains
               CATH domains 1hbrB00 B:1-144 Globins                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------S--------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---GLOBIN  PDB: B:4-144 UniProt: 5-147                                                                                                           PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1hbr B   1 VHWTAEEKQLITGLWGKVNVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPMVRAHGKKVLTSFGDAVKNLDNIKNTFSQLSELHCDKLHVDPENFRLLGDILIIVLAAHFSKDFTPECQAAWQKLVRVVAHALARK 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    


Chain C from PDB  Type:PROTEIN  Length:141
 aligned with HBAD_CHICK | P02001 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 
           HBAD_CHICK     1 MLTAEDKKLIQQAWEKAASHQEEFGAEALTRMFTTYPQTKTYFPHFDLSPGSDQVRGHGKKVLGALGNAVKNVDNLSQAMAELSNLHAYNLRVDPVNFKLLSQCIQVVLAVHMGKDYTPEVHAAFDKFLSAVSAVLAEKYR 141
               SCOP domains d1hbrc_ C: Hemoglobin, alpha-chain                                                                                                            SCOP domains
               CATH domains 1hbrC00 C:1-141 Globins                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhh..........hhhhhhhhhhhhhhhhhhh....hhhh.hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: C:2-141 UniProt: 2-141                                                                                                          PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hbr C   1 MLTAEDKKLIQQAWEKAASHQEEFGAEALTRMFTTYPQTKTYFPHFDLSPGSDQVRGHGKKVLGALGNAVKNVDNLSQAMAELSNLHAYNLRVDPVNFKLLSQCIQVVLAVHMGKDYTPEVHAAFDKFLSAVSAVLAEKYR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 


Chain D from PDB  Type:PROTEIN  Length:146
 aligned with HBB_CHICK | P02112 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      
            HBB_CHICK     2 VHWTAEEKQLITGLWGKVNVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPMVRAHGKKVLTSFGDAVKNLDNIKNTFSQLSELHCDKLHVDPENFRLLGDILIIVLAAHFSKDFTPECQAAWQKLVRVVAHALARKYH 147
               SCOP domains d1hbrd_ D: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 1hbrD00 D:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------S----------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---GLOBIN  PDB: D:4-146 UniProt: 5-147                                                                                                             PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hbr D   1 VHWTAEEKQLITGLWGKVNVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPMVRAHGKKVLTSFGDAVKNLDNIKNTFSQLSELHCDKLHVDPENFRLLGDILIIVLAAHFSKDFTPECQAAWQKLVRVVAHALARKYH 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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HBR)

(-) Gene Ontology  (10, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (HBAD_CHICK | P02001)
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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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,D   (HBB_CHICK | P02112)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0030492    hemoglobin binding    Interacting selectively and non-covalently with hemoglobin, an oxygen carrying, conjugated protein containing four heme groups and globin.
    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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  1hbr
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 Related Entries

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