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(-) Description

Title :  CRYSTAL STRUCTURE DETERMINATION OF LEPUS EUROPAEUS 2.8 A RESOLUTION
 
Authors :  M. Thenmozhi, Pon. Sathya Moothy, M. Balasubramanian, M. N. Ponnuswa
Date :  09 Feb 10  (Deposition) - 09 Feb 11  (Release) - 09 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Lepus Europaeus, Monoclinic, Oxygen Tranport/Storage, Heme, Iron, Metal-Binding, Oxygen Binding, High Oxygen Affinity, Oxygen Transport, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Pon. Sathya Moothy, M. Thenmozhi, M. Balasubramanian, M. N. Ponnuswamy
Crystal Structure Determination Of Lepus Europaeus 2. 8 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HEMOGLOBIN SUBUNIT ALPHA
    Chains: A, C
    Organism Common: EUROPEAN HARE
    Organism Scientific: LEPUS EUROPAEUS
    Organism Taxid: 9983
    Synonym: HEMOGLOBIN ALPHA CHAIN, ALPHA-GLOBIN
    Tissue: RED BLOOD CELLS
 
Molecule 2 - HEMOGLOBIN SUBUNIT BETA
    Chains: B, D
    Organism Common: EUROPEAN HARE
    Organism Scientific: LEPUS EUROPAEUS
    Organism Taxid: 9983
    Synonym: HEMOGLOBIN BETA CHAIN, BETA-GLOBIN
    Tissue: RED BLOOD CELLS

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2OXY4Ligand/IonOXYGEN MOLECULE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:42 , HIS A:45 , HIS A:58 , LYS A:61 , ALA A:65 , LEU A:86 , HIS A:87 , LEU A:91 , VAL A:93 , ASN A:97 , PHE A:98 , LEU A:101 , OXY A:143 , LYS D:66BINDING SITE FOR RESIDUE HEM A 142
2AC2SOFTWAREPHE A:43 , HIS A:58 , VAL A:62 , HEM A:142BINDING SITE FOR RESIDUE OXY A 143
3AC3SOFTWAREPHE B:41 , LYS B:66 , ALA B:70 , PHE B:71 , LEU B:88 , HIS B:92 , LEU B:96 , VAL B:98 , ASN B:102 , LEU B:106 , OXY B:148 , ARG C:141BINDING SITE FOR RESIDUE HEM B 147
4AC4SOFTWAREHIS B:63 , VAL B:67 , HEM B:147BINDING SITE FOR RESIDUE OXY B 148
5AC5SOFTWARETYR C:42 , PHE C:43 , HIS C:45 , PHE C:46 , HIS C:58 , LYS C:61 , VAL C:62 , LEU C:83 , HIS C:87 , LEU C:91 , VAL C:93 , ASN C:97 , PHE C:98 , LEU C:101 , OXY C:143BINDING SITE FOR RESIDUE HEM C 142
6AC6SOFTWAREHIS C:58 , HEM C:142BINDING SITE FOR RESIDUE OXY C 143
7AC7SOFTWARELYS A:90 , THR D:38 , PHE D:41 , PHE D:42 , HIS D:63 , LYS D:66 , LEU D:88 , HIS D:92 , LEU D:96 , VAL D:98 , ASN D:102 , PHE D:103 , LEU D:106 , LEU D:141 , OXY D:148BINDING SITE FOR RESIDUE HEM D 147
8AC8SOFTWAREHIS D:63 , VAL D:67 , HEM D:147BINDING SITE FOR RESIDUE OXY D 148

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LQD)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBB_LEPEU2-147
 		  2B:1-146
D:1-146

(-) Exons   (0, 0)

(no "Exon" information available for 3LQD)

(-) 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 F2Z285_LEPEU | F2Z285 from UniProtKB/TrEMBL  Length:141

    Alignment length:141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 
         F2Z285_LEPEU     1 VLSPADKTNIKTAWEKIGSHGGEYGAEAVERMFLGFPTTKTYFPHFDFTHGSEQIKAHGKKVSEALTKAVGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLANHHPSEFTPAVHASLDKFLANVSTVLTSKYR 141
               SCOP domains d3lqda_ A: automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lqd A   1 VLSPADKTNIKTAWEKIGSHGGEYGAEAVERMFLGFPTTKTYFPHFDFTHGSEQIKAHGKKVSEALTKAVGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLANHHPSEFTPAVHASLDKFLANVSTVLTSKYR 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_LEPEU | P08535 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      
            HBB_LEPEU     2 VHLSGEEKSAVTALWGKVNVEEVGGETLGRLLVVYPWTQRFFESFGDLSTASAVMGNPKVKAHGKKVLAAFSEGLSHLDNLKGTFAKLSELHCDKLHVDPENFRLLGNVLVIVLSHHFGKEFTPQVQAAYQKVVAGVANALAHKYH 147
               SCOP domains d3lqdb_ B: automated matches                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GLOBIN  PDB: B:1-146 UniProt: 2-147                                                                                                                PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lqd B   1 VHLSGEEKSAVTALWGKVNVEEVGGETLGRLLVVYPWTQRFFESFGDLSTASAVMGNPKVKAHGKKVLAAFSEGLSHLDNLKGTFAKLSELHCDKLHVDPENFRLLGNVLVIVLSHHFGKEFTPQVQAAYQKVVAGVANALAHKYH 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 F2Z285_LEPEU | F2Z285 from UniProtKB/TrEMBL  Length:141

    Alignment length:141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 
         F2Z285_LEPEU     1 VLSPADKTNIKTAWEKIGSHGGEYGAEAVERMFLGFPTTKTYFPHFDFTHGSEQIKAHGKKVSEALTKAVGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLANHHPSEFTPAVHASLDKFLANVSTVLTSKYR 141
               SCOP domains d3lqdc_ C: automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lqd C   1 VLSPADKTNIKTAWEKIGSHGGEYGAEAVERMFLGFPTTKTYFPHFDFTHGSEQIKAHGKKVSEALTKAVGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLANHHPSEFTPAVHASLDKFLANVSTVLTSKYR 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_LEPEU | P08535 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      
            HBB_LEPEU     2 VHLSGEEKSAVTALWGKVNVEEVGGETLGRLLVVYPWTQRFFESFGDLSTASAVMGNPKVKAHGKKVLAAFSEGLSHLDNLKGTFAKLSELHCDKLHVDPENFRLLGNVLVIVLSHHFGKEFTPQVQAAYQKVVAGVANALAHKYH 147
               SCOP domains d3lqdd_ D: automated matches                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------Globin-3lqdD01 D:7-111                                                                                   ----------------------------------- Pfam domains (1)
           Pfam domains (2) ------Globin-3lqdD02 D:7-111                                                                                   ----------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GLOBIN  PDB: D:1-146 UniProt: 2-147                                                                                                                PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lqd D   1 VHLSGEEKSAVTALWGKVNVEEVGGETLGRLLVVYPWTQRFFESFGDLSTASAVMGNPKVKAHGKKVLAAFSEGLSHLDNLKGTFAKLSELHCDKLHVDPENFRLLGNVLVIVLSHHFGKEFTPQVQAAYQKVVAGVANALAHKYH 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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LQD)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (8, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (F2Z285_LEPEU | F2Z285)
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_LEPEU | P08535)
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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