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(-) Description

Title :  THE CRYSTAL STRUCTURE OF TREMATOMUS BERNACCHII HEMOGLOBIN OXIDIZED BY AIR
 
Authors :  L. Vitagliano, G. Bonomi, A. Riccio, G. Di Prisco, G. Smulevich, L. Mazzarella
Date :  22 Jan 04  (Deposition) - 04 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Hemichrome, Bis-Histidine, Oxidation, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Vitagliano, G. Bonomi, A. Riccio, G. Di Prisco, G. Smulevich, L. Mazzarella
The Oxidation Process Of Antarctic Fish Hemoglobins
Eur. J. Biochem. V. 271 1651 2004
PubMed-ID: 15096204  |  Reference-DOI: 10.1111/J.1432-1033.2004.04054.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOGLOBIN ALPHA CHAIN
    Chains: A
    Organism Common: EMERALD ROCKCOD
    Organism Scientific: TREMATOMUS BERNACCHII
    Organism Taxid: 40690
 
Molecule 2 - HEMOGLOBIN BETA CHAIN
    Chains: B
    Organism Common: EMERALD ROCKCOD
    Organism Scientific: TREMATOMUS BERNACCHII
    Organism Taxid: 40690

 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, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:32 , TYR A:42 , HIS A:45 , HIS A:59 , LYS A:62 , LEU A:84 , GLN A:87 , HIS A:88 , LEU A:92 , VAL A:94 , ASN A:98 , LEU A:102 , LEU A:137 , HOH A:500BINDING SITE FOR RESIDUE HEM A 200
2AC2SOFTWAREHIS B:41 , PHE B:42 , HIS B:63 , LYS B:66 , LEU B:88 , LEU B:91 , HIS B:92 , LEU B:96 , ASN B:102 , PHE B:103 , LEU B:106 , LEU B:141BINDING SITE FOR RESIDUE HEM B 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S5X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S5X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S5X)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBA_TREBE2-142  1A:2-142
HBB_TREBE5-147  1B:4-144
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBA_TREBE2-142  2A:2-142
HBB_TREBE5-147  2B:4-144

(-) Exons   (0, 0)

(no "Exon" information available for 1S5X)

(-) 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:143
 aligned with HBA_TREBE | P80043 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:143
                             1                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139   
            HBA_TREBE     - -SLSDKDKAAVRALWSKIGKSADAIGNDALSRMIVVYPQTKTYFSHWPDVTPGSPHIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPANFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR 142
               SCOP domains d1s5xa_ A: Hemoglobin, alpha-chain                                                                                                              SCOP domains
               CATH domains -1s5xA00 A:1-142 Globins                                                                                                                        CATH domains
               Pfam domains ------Globin-1s5xA01 A:6-107                                                                                ----------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: A:2-142 UniProt: 2-142                                                                                                           PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s5x A   0 xSLSDKDKAAVRALWSKIGKSADAIGNDALSRMIVVYPQTKTYFSHWPDVTPGSPHIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPANFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR 142
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139   
                            |                                                                                                                                              
                            0-ACE                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:136
 aligned with HBB_TREBE | P80044 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:144
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141    
            HBB_TREBE     2 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLIVYPWTQRHFSGFGNLYNAEAIIGNANVAAHGIKVLHGLDRGVKNMDNIAATYADLSTLHSEKLHVDPDNFKLLSDCITIVLAAKMGHAFTAETQGAFQKFLAVVVSALGKQ 145
               SCOP domains d1s5xb_ B: Hemoglobin, beta-chain                                                                                                                SCOP domains
               CATH domains 1s5xB00 B:1-144 Globins                                                                                                                          CATH domains
               Pfam domains ------Globin-1s5xB01 B:7-111                                                                                   --------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.--------....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ---GLOBIN  PDB: B:4-144 UniProt: 5-147                                                                                                           PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1s5x B   1 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLIVYPWTQRHFSG--------AIIGNANVAAHGIKVLHGLDRGVKNMDNIAATYADLSTLHSEKLHVDPDNFKLLSDCITIVLAAKMGHAFTAETQGAFQKFLAVVVSALGKQ 144
                                    10        20        30        40   |     -  |     60        70        80        90       100       110       120       130       140    
                                                                      44       53
   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_TREBE | P80043)
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_TREBE | P80044)
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
        HBA_TREBE | P80043: 1hbh 1pbx 1s5y 2h8d 2h8f 2peg 3gkv 3gqg 4g51 4iro 4odc
        HBB_TREBE | P80044: 1hbh 1pbx 1s5y 2h8d 2h8f 2peg 3gkv 3gqg 4g51 4iro 4odc

(-) Related Entries Specified in the PDB File

1la6
1s5y THE SAME PROTEIN OXIDIZED BY FERRICYANIDE