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(-) Description

Title :  HORSE METHEMOGLOBIN LOW SALT, PH 7.0 (88% RELATIVE HUMIDITY)
 
Authors :  R. Sankaranarayanan, B. K. Biswal, M. Vijayan
Date :  13 Dec 04  (Deposition) - 26 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Aquo Methemoglobin, Quarternary Association, Allosteric Transition, Protein Hydration, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Sankaranarayanan, B. K. Biswal, M. Vijayan
A New Relaxed State In Horse Methemoglobin Characterized By Crystallographic Studies.
Proteins V. 60 547 2005
PubMed-ID: 15887226  |  Reference-DOI: 10.1002/PROT.20510
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOGLOBIN ALPHA CHAINS
    ChainsA, C
    Organism CommonHORSE
    Organism ScientificEQUUS CABALLUS
    Organism Taxid9796
    Other DetailsPH 7.0 AQUOMET STRUCTURE
    SynonymSLOW AND FAST
 
Molecule 2 - HEMOGLOBIN BETA CHAIN
    ChainsB, D
    Organism CommonHORSE
    Organism ScientificEQUUS CABALLUS
    Organism Taxid9796

 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 , HIS A:87 , LEU A:91 , VAL A:93 , PHE A:98 , LEU A:101 , HOH A:439 , HOH A:900BINDING SITE FOR RESIDUE HEM A 142
2AC2SOFTWARELYS A:90 , ARG A:141 , PHE B:41 , PHE B:42 , HIS B:63 , LYS B:66 , SER B:70 , PHE B:71 , LEU B:88 , HIS B:92 , LEU B:96 , ASN B:102 , LEU B:106 , LEU B:141 , HOH B:901BINDING SITE FOR RESIDUE HEM B 147
3AC3SOFTWARETYR C:42 , PHE C:43 , HIS C:45 , HIS C:58 , LYS C:61 , HIS C:87 , LEU C:91 , ASN C:97 , PHE C:98 , LEU C:101 , HOH C:902BINDING SITE FOR RESIDUE HEM C 142
4AC4SOFTWARELYS C:11 , PHE D:41 , PHE D:42 , HIS D:63 , SER D:70 , PHE D:71 , HIS D:92 , LEU D:96 , ASN D:102 , LEU D:141 , HOH D:231 , HOH D:477 , HOH D:903BINDING SITE FOR RESIDUE HEM D 147

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y8K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y8K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric/Biological Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_HBA_HORSE_001 *Y25FHBA_HORSE  ---  ---A/CY24F
2UniProtVAR_HBA_HORSE_002 *K61QHBA_HORSE  ---  ---A/CK60Q
   * 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.HBA_HORSE3-142
 
  2A:2-141
C:2-141
HBB_HORSE3-146
 
  2B:3-146
D:3-146

(-) Exons   (0, 0)

(no "Exon" information available for 1Y8K)

(-) 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 HBA_HORSE | P01958 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
            HBA_HORSE     2 VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSKYR 142
               SCOP domains d1y8ka_ A: Hemoglobin, alpha-chain                                                                                                            SCOP domains
               CATH domains 1y8kA00 A:1-141 Globins                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------F-----------------------------------Q--------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -GLOBIN  PDB: A:2-141 UniProt: 3-142                                                                                                          PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y8k A   1 VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSDLSNLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSKYR 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_HORSE | P02062 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
            HBB_HORSE     1 VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH 146
               SCOP domains d1y8kb_ B: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 1y8kB00 B:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: B:3-146 UniProt: 3-146                                                                                                              PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y8k B   1 VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      

Chain C from PDB  Type:PROTEIN  Length:141
 aligned with HBA_HORSE | P01958 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
            HBA_HORSE     2 VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSKYR 142
               SCOP domains d1y8kc_ C: Hemoglobin, alpha-chain                                                                                                            SCOP domains
               CATH domains 1y8kC00 C:1-141 Globins                                                                                                                       CATH domains
           Pfam domains (1) -----Globin-1y8kC01 C:6-106                                                                               ----------------------------------- Pfam domains (1)
           Pfam domains (2) -----Globin-1y8kC02 C:6-106                                                                               ----------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------F-----------------------------------Q--------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -GLOBIN  PDB: C:2-141 UniProt: 3-142                                                                                                          PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y8k C   1 VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSDLSNLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSKYR 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_HORSE | P02062 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
            HBB_HORSE     1 VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH 146
               SCOP domains d1y8kd_ D: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 1y8kD00 D:1-146 Globins                                                                                                                            CATH domains
           Pfam domains (1) ------Globin-1y8kD01 D:7-111                                                                                   ----------------------------------- Pfam domains (1)
           Pfam domains (2) ------Globin-1y8kD02 D:7-111                                                                                   ----------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: D:3-146 UniProt: 3-146                                                                                                              PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y8k D   1 VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH 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

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: Globin (291)

(-) Gene Ontology  (8, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (HBA_HORSE | P01958)
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   (HBB_HORSE | P02062)
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_HORSE | P019581g0b 1ibe 1iwh 1ns6 1ns9 1y8h 1y8i 2d5x 2dhb 2mhb 2zlt 2zlu 2zlv 2zlw 2zlx 5c6e
        HBB_HORSE | P020621g0b 1ibe 1iwh 1ns6 1ns9 1y8h 1y8i 2d5x 2dhb 2mhb 2zlt 2zlu 2zlv 2zlw 2zlx 5c6e

(-) Related Entries Specified in the PDB File

1jy7 1lfq 1y8h 1y8i