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(-) Description

Title :  CARBONMONOXY HEMOGLOBIN FROM THE TELEOST FISH LEIOSTOMUS XANTHURUS
 
Authors :  S. E. Mylvaganam, E. D. Getzoff
Date :  05 Feb 96  (Deposition) - 12 Mar 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Carbon Monoxide, R-State, Leiostomus Xanthurus, Teleost Fish, Root Effect, Globin, Oxygen Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. E. Mylvaganam, C. Bonaventura, J. Bonaventura, E. D. Getzoff
Structural Basis For The Root Effect In Haemoglobin.
Nat. Struct. Biol. V. 3 275 1996
PubMed-ID: 8605630  |  Reference-DOI: 10.1038/NSB0396-275
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOGLOBIN
    Chains: A
    Organism Common: SPOT CROAKER
    Organism Scientific: LEIOSTOMUS XANTHURUS
    Organism Taxid: 59837
    Other Details: R-STATE, CARBONMONOXY BOUND ROOT EFFECT HEMOGLOBIN
    Synonym: SPOT HEMOGLOBIN, SPOTHBCO
    Tissue: BLOOD
 
Molecule 2 - HEMOGLOBIN
    Chains: B
    Organism Common: SPOT CROAKER
    Organism Scientific: LEIOSTOMUS XANTHURUS
    Organism Taxid: 59837
    Other Details: R-STATE, CARBONMONOXY BOUND ROOT EFFECT HEMOGLOBIN
    Synonym: SPOT HEMOGLOBIN, SPOTHBCO
    Tissue: BLOOD

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2CMO2Ligand/IonCARBON MONOXIDE
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2CMO4Ligand/IonCARBON MONOXIDE
3HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:42 , PHE A:43 , TRP A:46 , HIS A:60 , VAL A:63 , ILE A:64 , ALA A:67 , VAL A:68 , HIS A:89 , VAL A:95 , ASN A:99 , PHE A:100 , LEU A:103 , LEU A:134 , CMO A:145 , HOH A:311 , THR B:4 , ASP B:5BINDING SITE FOR RESIDUE HEM A 144
2AC2SOFTWAREHIS A:60 , ILE A:64 , HEM A:144BINDING SITE FOR RESIDUE CMO A 145
3AC3SOFTWAREHIS B:41 , HIS B:63 , THR B:66 , HIS B:92 , ILE B:96 , VAL B:98 , ASN B:102 , LEU B:142 , CMO B:149 , HOH B:353BINDING SITE FOR RESIDUE HEM B 148
4AC4SOFTWAREHIS B:63 , VAL B:67 , HEM B:148BINDING SITE FOR RESIDUE CMO B 149

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBA_LEIXA2-143  1A:2-143
HBB_LEIXA4-147  1B:4-147
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBA_LEIXA2-143  2A:2-143
HBB_LEIXA4-147  2B:4-147

(-) Exons   (0, 0)

(no "Exon" information available for 1SPG)

(-) 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:144
 aligned with HBA_LEIXA | P56250 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:144
                             1                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139    
            HBA_LEIXA     - -SLSATDKARVKALWDKIEGKSAELGAEALGRMLVSFPQTKIYFSEWGQDLGPQTPQVRNHGAVIMAAVGKAVKSIDNLVGGLSQLSELHAFKLRVDPANFKILAHNIILVISMYFPGDFTPEVHLSVDKFLACLALALSEKYR 143
               SCOP domains d1spga_ A: Hemoglobin, alpha-chain                                                                                                               SCOP domains
               CATH domains -1spgA00 A:1-143 Globins                                                                                                                         CATH domains
               Pfam domains ------Globin-1spgA01 A:6-108                                                                                 ----------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh........hhhhhhhhh.....hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: A:2-143 UniProt: 2-143                                                                                                            PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1spg A   0 xSLSATDKARVKALWDKIEGKSAELGAEALGRMLVSFPQTKIYFSEWGQDLGPQTPQVRNHGAVIMAAVGKAVKSIDNLVGGLSQLSELHAFKLRVDPANFKILAHNIILVISMYFPGDFTPEVHLSVDKFLACLALALSEKYR 143
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139    
                            |                                                                                                                                               
                            0-ACE                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:147
 aligned with HBB_LEIXA | P56251 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
            HBB_LEIXA     1 VDWTDAERAAIKALWGKIDVGEIGPQALSRLLIVYPWTQRHFKGFGNISTNAAILGNAKVAEHGKTVMGGLDRAVQNMDNIKNVYKQLSIKHSEKIHVDPDNFRLLGEIITMCVGAKFGPSAFTPEIHEAWQKFLAVVVSALGRQYH 147
               SCOP domains d1spgb_ B: Hemoglobin, beta-chain                                                                                                                   SCOP domains
               CATH domains 1spgB00 B:1-147 Globins                                                                                                                             CATH domains
               Pfam domains ------Globin-1spgB01 B:7-111                                                                                   ------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhh.....hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---GLOBIN  PDB: B:4-147 UniProt: 4-147                                                                                                              PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1spg B   1 VDWTDAERAAIKALWGKIDVGEIGPQALSRLLIVYPWTQRHFKGFGNISTNAAILGNAKVAEHGKTVMGGLDRAVQNMDNIKNVYKQLSIKHSEKIHVDPDNFRLLGEIITMCVGAKFGPSAFTPEIHEAWQKFLAVVVSALGRQYH 147
                                    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  (1, 2)

Asymmetric Unit
(-)
Clan: Globin (291)

(-) Gene Ontology  (8, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (HBA_LEIXA | P56250)
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_LEIXA | P56251)
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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