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(-) Description

Title :  CRYSTAL STRUCTURE DETERMINATION OF GOAT HEMOGLOBIN (CAPRA HIRCUS) AT 3 ANGSTROM RESOLUTION
 
Authors :  Pon. Sathya Moorthy, K. Neelagandan, M. Balasubramanian, M. N. Ponnuswamy
Date :  09 Oct 08  (Deposition) - 10 Nov 09  (Release) - 10 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Low Oxygen Affinity, Capra Hircus, Hemoglobin, Allosteric Mechanism, 2, 3-Diphospho Glycerate, Oxygen Storage, Oxygen Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Pon. Sathya Moorthy, K. Neelagandan, M. Balasubramanian, M. N. Ponnuswamy
Purification, Crystallization And Preliminary X-Ray Diffraction Studies On Goat (Capra Hircus) Hemoglobin - A Low Oxygen Affinity Species
Protein Pept. Lett. V. 16 454 2009
PubMed-ID: 19356147  |  Reference-DOI: 10.2174/092986609787847992
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOGLOBIN SUBUNIT ALPHA-1/2
    CellRED BLOOD CELLS
    ChainsA, C
    Organism CommonDOMESTIC GOAT, GOATS
    Organism ScientificCAPRA HIRCUS
    Organism Taxid9925
    SynonymHEMOGLOBIN ALPHA-1/2 CHAIN, ALPHA-1/2-GLOBIN
    TissueBLOOD
 
Molecule 2 - HEMOGLOBIN SUBUNIT BETA-A
    CellRED BLOOD CELLS
    ChainsB, D
    Organism CommonDOMESTIC GOAT, GOATS
    Organism ScientificCAPRA HIRCUS
    Organism Taxid9925
    SynonymHEMOGLOBIN BETA-A CHAIN, BETA-A-GLOBIN, ALANINE BETA-GLOBIN
    TissueBLOOD

 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
1AC1SOFTWARETHR A:39 , TYR A:42 , PHE A:43 , HIS A:45 , HIS A:58 , LYS A:61 , 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:136BINDING SITE FOR RESIDUE HEM A 142
2AC2SOFTWAREPHE B:41 , PHE B:42 , HIS B:44 , PHE B:45 , HIS B:63 , VAL B:67 , SER B:70 , LEU B:88 , LEU B:91 , HIS B:92 , LEU B:96 , VAL B:98 , ASN B:102 , LEU B:106BINDING SITE FOR RESIDUE HEM B 147
3AC3SOFTWARETYR C:42 , PHE C:43 , HIS C:45 , HIS C:58 , VAL C:62 , LEU C:83 , HIS C:87 , LEU C:91 , LEU C:101BINDING SITE FOR RESIDUE HEM C 142
4AC4SOFTWAREPHE D:41 , PHE D:42 , HIS D:44 , HIS D:63 , LYS D:66 , SER D:70 , LEU D:91 , HIS D:92 , LEU D:96 , VAL D:98 , ASN D:102 , LEU D:106 , LEU D:141BINDING SITE FOR RESIDUE HEM D 147

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EU1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EU1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 10)

Asymmetric/Biological Unit (5, 10)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_HBBA_CAPHI_001 *D20HHBBA_CAPHI  ---  ---B/DD21H
2UniProtVAR_HBA1_CAPHI_001 *D76YHBA1_CAPHI  ---  ---A/CD75Y
3UniProtVAR_HBBA_CAPHI_002 *Q86HHBBA_CAPHI  ---  ---B/DQ87H
4UniProtVAR_HBBA_CAPHI_003 *K103RHBBA_CAPHI  ---  ---B/DK104R
5UniProtVAR_HBBA_CAPHI_004 *L124VHBBA_CAPHI  ---  ---B/DL125V
   * 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.HBBA_CAPHI2-145
 
  2B:3-146
D:3-146
HBA2_CAPHI3-142
 
  2A:2-141
C:2-141
HBA1_CAPHI3-142
 
  2A:2-141
C:2-141

(-) Exons   (0, 0)

(no "Exon" information available for 3EU1)

(-) 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 HBA1_CAPHI | P0CH25 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
           HBA1_CAPHI     2 VLSAADKSNVKAAWGKVGGNAGAYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGEKVAAALTKAVGHLDDLPGTLSDLSDLHAHKLRVDPVNFKLLSHSLLVTLACHLPNDFTPAVHASLDKFLANVSTVLTSKYR 142
               SCOP domains d3eu1a_ A: automated matches                                                                                                                  SCOP domains
               CATH domains 3eu1A00 A:1-141 Globins                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------Y------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -GLOBIN  PDB: A:2-141 UniProt: 3-142                                                                                                          PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eu1 A   1 VLSAADKSNVKAAWGKVGGNAGAYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGEKVAAALTKAVGHLDDLPGTLSDLSDLHAHKLRVDPVNFKLLSHSLLVTLACHLPNDFTPAVHASLDKFLANVSTVLTSKYR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 

Chain A from PDB  Type:PROTEIN  Length:141
 aligned with HBA2_CAPHI | P0CH26 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
           HBA2_CAPHI     2 VLSAADKSNVKAAWGKVGSNAGAYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGEKVAAALTKAVGHLDDLPGTLSDLSDLHAHKLRVDPVNFKLLSHSLLVTLACHHPSDFTPAVHASLDKFLANVSTVLTSKYR 142
               SCOP domains d3eu1a_ A: automated matches                                                                                                                  SCOP domains
               CATH domains 3eu1A00 A:1-141 Globins                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------Y------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -GLOBIN  PDB: A:2-141 UniProt: 3-142                                                                                                          PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eu1 A   1 VLSAADKSNVKAAWGKVGGNAGAYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGEKVAAALTKAVGHLDDLPGTLSDLSDLHAHKLRVDPVNFKLLSHSLLVTLACHLPNDFTPAVHASLDKFLANVSTVLTSKYR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 

Chain B from PDB  Type:PROTEIN  Length:145
 aligned with HBBA_CAPHI | P02077 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     
           HBBA_CAPHI     1 MLTAEEKAAVTGFWGKVKVDEVGAEALGRLLVVYPWTQRFFEHFGDLSSADAVMNNAKVKAHGKKVLDSFSNGMKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVVVLARHHGSEFTPLLQAEFQKVVAGVANALAHRYH 145
               SCOP domains d3eu1b_ B: automated matches                                                                                                                      SCOP domains
               CATH domains 3eu1B00 B:2-146 Globins                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------H-----------------------------------------------------------------H----------------R--------------------V--------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: B:3-146 UniProt: 2-145                                                                                                              PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eu1 B   2 MLTAEEKAAVTGFWGKVKVDEVGAEALGRLLVVYPWTQRFFEHFGDLSSADAVMNNAKVKAHGKKVLDSFSNGMKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVVVLARHHGSEFTPLLQAEFQKVVAGVANALAHRYH 146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141     

Chain C from PDB  Type:PROTEIN  Length:141
 aligned with HBA1_CAPHI | P0CH25 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
           HBA1_CAPHI     2 VLSAADKSNVKAAWGKVGGNAGAYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGEKVAAALTKAVGHLDDLPGTLSDLSDLHAHKLRVDPVNFKLLSHSLLVTLACHLPNDFTPAVHASLDKFLANVSTVLTSKYR 142
               SCOP domains d3eu1c_ C: automated matches                                                                                                                  SCOP domains
               CATH domains 3eu1C00 C:1-141 Globins                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------Y------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -GLOBIN  PDB: C:2-141 UniProt: 3-142                                                                                                          PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eu1 C   1 VLSAADKSNVKAAWGKVGGNAGAYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGEKVAAALTKAVGHLDDLPGTLSDLSDLHAHKLRVDPVNFKLLSHSLLVTLACHLPNDFTPAVHASLDKFLANVSTVLTSKYR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 

Chain C from PDB  Type:PROTEIN  Length:141
 aligned with HBA2_CAPHI | P0CH26 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
           HBA2_CAPHI     2 VLSAADKSNVKAAWGKVGSNAGAYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGEKVAAALTKAVGHLDDLPGTLSDLSDLHAHKLRVDPVNFKLLSHSLLVTLACHHPSDFTPAVHASLDKFLANVSTVLTSKYR 142
               SCOP domains d3eu1c_ C: automated matches                                                                                                                  SCOP domains
               CATH domains 3eu1C00 C:1-141 Globins                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------Y------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -GLOBIN  PDB: C:2-141 UniProt: 3-142                                                                                                          PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eu1 C   1 VLSAADKSNVKAAWGKVGGNAGAYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGEKVAAALTKAVGHLDDLPGTLSDLSDLHAHKLRVDPVNFKLLSHSLLVTLACHLPNDFTPAVHASLDKFLANVSTVLTSKYR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 

Chain D from PDB  Type:PROTEIN  Length:145
 aligned with HBBA_CAPHI | P02077 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     
           HBBA_CAPHI     1 MLTAEEKAAVTGFWGKVKVDEVGAEALGRLLVVYPWTQRFFEHFGDLSSADAVMNNAKVKAHGKKVLDSFSNGMKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVVVLARHHGSEFTPLLQAEFQKVVAGVANALAHRYH 145
               SCOP domains d3eu1d_ D: automated matches                                                                                                                      SCOP domains
               CATH domains 3eu1D00 D:2-146 Globins                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------H-----------------------------------------------------------------H----------------R--------------------V--------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: D:3-146 UniProt: 2-145                                                                                                              PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eu1 D   2 MLTAEEKAAVTGFWGKVKVDEVGAEALGRLLVVYPWTQRFFEHFGDLSSADAVMNNAKVKAHGKKVLDSFSNGMKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVVVLARHHGSEFTPLLQAEFQKVVAGVANALAHRYH 146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141     

   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  (1, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EU1)

(-) Gene Ontology  (8, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (HBA1_CAPHI | P0CH25)
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 A,C   (HBA2_CAPHI | P0CH26)
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,D   (HBBA_CAPHI | P02077)
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
        HBA1_CAPHI | P0CH252ri4 3d1a
        HBA2_CAPHI | P0CH262ri4 3d1a
        HBBA_CAPHI | P020772ri4 3d1a

(-) Related Entries Specified in the PDB File

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2ri4 CRYSTAL STRUCTURE DETERMINATION OF GOAT METHEMOGLOBIN AT 2.7 ANGSTROM RESOLUTION
3cy5 CRYSTAL STRUCTURE DETERMINATION OF BUFFALO HEMOGLOBIN AT 2 ANGSTROM RESOLUTION
3d1a CRYSTAL STRUCTURE DETERMINATION OF GOAT HEMOGLOBIN AT 2.61 ANGSTROM RESOLUTION
3d4x CRYSTAL STRUCTURE DETERMINATION OF CAT HEMOGLOBIN AT 2.2 ANGSTROM RESOLUTION