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(-) Description

Title :  HORSE METHEMOGLOBIN HIGH SALT, PH 7.0 (66% RELATIVE HUMIDITY)
 
Authors :  P. S. Kaushal, R. Sankaranarayanan, M. Vijayan
Date :  10 Apr 08  (Deposition) - 24 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  C,D  (2x)
Biol. Unit 3:  B,D  (1x)
Biol. Unit 4:  A  (1x)
Biol. Unit 5:  C  (1x)
Keywords :  Protein Hydration, Allosteric Transitions, Variability In Quaternary Structure, Solvent Content And Crystal Structure, Water-Mediated Transformation, Heme, Iron, Metal-Binding, Oxygen Transport, Polymorphism, Transport, Oxygen Storage (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. S. Kaushal, R. Sankaranarayanan, M. Vijayan
Water-Mediated Variability In The Structure Of Relaxed-State Haemoglobin
Acta Crystallogr. , Sect. F V. 64 463 2008
PubMed-ID: 18540052  |  Reference-DOI: 10.1107/S1744309108013109
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOGLOBIN SUBUNIT ALPHA
    ChainsA, C
    Organism CommonHORSE
    Organism ScientificEQUUS CABALLUS
    Organism Taxid9796
    SynonymHEMOGLOBIN ALPHA CHAIN, ALPHA-GLOBIN
 
Molecule 2 - HEMOGLOBIN SUBUNIT BETA
    ChainsB, D
    Organism CommonHORSE
    Organism ScientificEQUUS CABALLUS
    Organism Taxid9796
    SynonymHEMOGLOBIN BETA CHAIN, BETA-GLOBIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (2x)AB  
Biological Unit 2 (2x)  CD
Biological Unit 3 (1x) B D
Biological Unit 4 (1x)A   
Biological Unit 5 (1x)  C 

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:42 , PHE A:43 , HIS A:45 , LYS A:61 , ALA A:65 , LEU A:83 , LEU A:86 , HIS A:87 , LEU A:91 , PHE A:98BINDING SITE FOR RESIDUE HEM A 142
2AC2SOFTWAREPHE B:41 , PHE B:42 , HIS B:63 , LYS B:66 , SER B:70 , PHE B:71 , LEU B:88 , HIS B:92 , ASN B:102 , LEU B:106 , LEU B:141 , LYS D:95BINDING SITE FOR RESIDUE HEM B 147
3AC3SOFTWAREGLU B:6 , TYR C:42 , PHE C:43 , HIS C:45 , HIS C:58 , LYS C:61 , ALA C:65 , LEU C:66 , LEU C:83 , HIS C:87 , LEU C:91 , PHE C:98 , LEU C:101 , LEU C:136BINDING SITE FOR RESIDUE HEM C 142
4AC4SOFTWAREASP B:43 , SER B:44 , PHE D:41 , PHE D:42 , HIS D:63 , LYS D:66 , SER D:70 , PHE D:71 , LEU D:88 , LEU D:91 , HIS D:92 , LEU D:96 , 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 2ZLX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZLX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric 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)
Biological Unit 1 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_HBA_HORSE_001 *Y25FHBA_HORSE  ---  ---AY24F
2UniProtVAR_HBA_HORSE_002 *K61QHBA_HORSE  ---  ---AK60Q
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_HBA_HORSE_001 *Y25FHBA_HORSE  ---  ---CY24F
2UniProtVAR_HBA_HORSE_002 *K61QHBA_HORSE  ---  ---CK60Q
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (0, 0)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 4 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_HBA_HORSE_001 *Y25FHBA_HORSE  ---  ---AY24F
2UniProtVAR_HBA_HORSE_002 *K61QHBA_HORSE  ---  ---AK60Q
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 5 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_HBA_HORSE_001 *Y25FHBA_HORSE  ---  ---CY24F
2UniProtVAR_HBA_HORSE_002 *K61QHBA_HORSE  ---  ---CK60Q
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBA_HORSE3-142
 
  2A:2-140
C:2-139
HBB_HORSE3-146
 
  2B:3-146
D:3-146
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBA_HORSE3-142
 
  2A:2-140
-
HBB_HORSE3-146
 
  2B:3-146
-
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBA_HORSE3-142
 
  2-
C:2-139
HBB_HORSE3-146
 
  2-
D:3-146
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBA_HORSE3-142
 
  0-
-
HBB_HORSE3-146
 
  2B:3-146
D:3-146
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBA_HORSE3-142
 
  1A:2-140
-
HBB_HORSE3-146
 
  0-
-
Biological Unit 5 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBA_HORSE3-142
 
  1-
C:2-139
HBB_HORSE3-146
 
  0-
-

(-) Exons   (0, 0)

(no "Exon" information available for 2ZLX)

(-) 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:140
 aligned with HBA_HORSE | P01958 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:140
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141
            HBA_HORSE     2 VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSKY 141
               SCOP domains d2zlxa_ A: Hemoglobin, alpha-chain                                                                                                           SCOP domains
               CATH domains 2zlxA00 A:1-140 Globins                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhh.......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------F-----------------------------------Q-------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -GLOBIN  PDB: A:2-140 UniProt: 3-142                                                                                                         PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zlx A   1 VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSDLSNLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSKY 140
                                    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 d2zlxb_ B: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 2zlxB00 B:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: B:3-146 UniProt: 3-146                                                                                                              PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zlx 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:139
 aligned with HBA_HORSE | P01958 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:139
                                    11        21        31        41        51        61        71        81        91       101       111       121       131         
            HBA_HORSE     2 VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSK 140
               SCOP domains d2zlxc_ C: Hemoglobin, alpha-chain                                                                                                          SCOP domains
               CATH domains 2zlxC00 C:1-139 Globins                                                                                                                     CATH domains
           Pfam domains (1) -----Globin-2zlxC01 C:6-106                                                                               --------------------------------- Pfam domains (1)
           Pfam domains (2) -----Globin-2zlxC02 C:6-106                                                                               --------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------F-----------------------------------Q------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -GLOBIN  PDB: C:2-139 UniProt: 3-142                                                                                                        PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zlx C   1 VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSDLSNLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSK 139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         

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 d2zlxd_ D: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 2zlxD00 D:1-146 Globins                                                                                                                            CATH domains
           Pfam domains (1) ------Globin-2zlxD01 D:7-111                                                                                   ----------------------------------- Pfam domains (1)
           Pfam domains (2) ------Globin-2zlxD02 D:7-111                                                                                   ----------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: D:3-146 UniProt: 3-146                                                                                                              PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zlx 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 Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Globin (291)

(-) Gene Ontology  (8, 16)

Asymmetric 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 1y8k 2d5x 2dhb 2mhb 2zlt 2zlu 2zlv 2zlw 5c6e
        HBB_HORSE | P020621g0b 1ibe 1iwh 1ns6 1ns9 1y8h 1y8i 1y8k 2d5x 2dhb 2mhb 2zlt 2zlu 2zlv 2zlw 5c6e

(-) Related Entries Specified in the PDB File

1jy7
1lfl
1lfq
1y8h
1y8i
1y8k
2zlt HORSE METHEMOGLOBIN HIGH SALT, PH 7.0
2zlu HORSE METHEMOGLOBIN HIGH SALT, PH 7.0 (88% RELATIVE HUMIDITY)
2zlv HORSE METHEMOGLOBIN HIGH SALT, PH 7.0 (79% RELATIVE HUMIDITY)
2zlw HORSE METHEMOGLOBIN HIGH SALT, PH 7.0 (75% RELATIVE HUMIDITY)