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(-) Description

Title :  MACROMOLECULAR STRUCTURE REFINEMENT BY RESTRAINED LEAST-SQUARES AND INTERACTIVE GRAPHICS AS APPLIED TO SICKLING DEER TYPE III HEMOGLOBIN
 
Authors :  E. L. Amma, R. L. Girling
Date :  01 Oct 79  (Deposition) - 07 Dec 79  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxygen Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. L. Girling, T. E. Houston, W. C. Schmidtjunior, E. L. Amma
Macromolecular Structure Refinement By Restrained Least-Squares And Interactive Graphics As Applied To Sickling Deer Type Iii Hemoglobin
Acta Crystallogr. , Sect. A V. 36 43 1980
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOGLOBIN S (DEOXY) (ALPHA CHAIN)
    Chains: A, C
    Engineered: YES
    Organism Common: WHITE-TAILED DEER
    Organism Scientific: ODOCOILEUS VIRGINIANUS
    Organism Taxid: 9874
 
Molecule 2 - HEMOGLOBIN S (DEOXY) (BETA CHAIN)
    Chains: B, D
    Engineered: YES
    Organism Common: WHITE-TAILED DEER
    Organism Scientific: ODOCOILEUS VIRGINIANUS
    Organism Taxid: 9874

 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
1AC1SOFTWARETHR A:39 , TYR A:42 , PHE A:43 , HIS A:58 , LYS A:61 , VAL A:62 , LEU A:86 , HIS A:87 , LEU A:91 , VAL A:93 , ASN A:97 , LEU A:136BINDING SITE FOR RESIDUE HEM A 142
2AC2SOFTWAREPHE B:40 , HIS B:43 , HIS B:62 , ARG B:65 , PHE B:84 , HIS B:91 , LEU B:95 , VAL B:97 , ASN B:101 , PHE B:102 , LEU B:105BINDING SITE FOR RESIDUE HEM B 146
3AC3SOFTWARETHR C:39 , TYR C:42 , PHE C:43 , HIS C:45 , HIS C:58 , LEU C:83 , LEU C:86 , HIS C:87 , LEU C:91 , VAL C:93 , ASN C:97 , LEU C:101 , ASP C:132BINDING SITE FOR RESIDUE HEM C 142
4AC4SOFTWAREPHE D:40 , HIS D:43 , HIS D:62 , VAL D:66 , HIS D:91 , LYS D:94 , LEU D:95 , ASN D:101 , PHE D:102 , LEU D:105BINDING SITE FOR RESIDUE HEM D 146

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (17, 17)

Asymmetric/Biological Unit
No.Residues
1Ala A:88 -His A:89
2Leu B:77 -Asp B:78
3Asp B:79 -Leu B:80
4Leu B:80 -Lys B:81
5Ala B:85 -Gln B:86
6Phe B:121 -Thr B:122
7Leu C:48 -Ser C:49
8Ser C:49 -His C:50
9Gln C:70 -Gly C:71
10Asn C:85 -Leu C:86
11Leu C:109 -Ala C:110
12Ala D:4 -Glu D:5
13Lys D:7 -Ala D:8
14Thr D:11 -Gly D:12
15Ala D:50 -Gly D:51
16Phe D:70 -Thr D:71
17Leu D:77 -Asp D:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric/Biological Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_HBA_ODOVI_001 *A5THBA_ODOVI  ---  ---A/CA5T
2UniProtVAR_HBA_ODOVI_002 *N20KHBA_ODOVI  ---  ---A/CN20K
3UniProtVAR_HBA_ODOVI_003 *Y24FHBA_ODOVI  ---  ---A/CY24F
   * 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_ODOVI2-141
 		  2A:2-141
C:2-141
HBB_ODOVI2-145
 		  2B:2-145
D:2-145

(-) Exons   (0, 0)

(no "Exon" information available for 1HDS)

(-) 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_ODOVI | P01972 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 
            HBA_ODOVI     1 VLSAABKSBVKAAWGKVGGNAAPYGAZALZRMFLSFPTTKTYFPHFBLSHGSAZVKAHGZKVABALTKAVGHLBBLPGTLSBLSBLHAHKLRVBPVBFKLLSHSLLVTLATHLPBBFTPAVHASLBKFLABVSTVLTSKYR 141
               SCOP domains d1hdsa_ A: Hemoglobin, alpha-chain                                                                                                            SCOP domains
               CATH domains 1hdsA00 A:1-141 Globins                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.....hhhhhhhhh.........hhhhh.........hhhhhhhhhhhhhhhhhh....hhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----T--------------K---F--------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: A:2-141 UniProt: 2-141                                                                                                          PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hds A   1 VLSAANKSNVKAAWGKVGGNAPAYGAQALQRMFLSFPTTKTYFPHFDLSHGSAQQKAHGQKVANALTKAQGHLNDLPGTLSNLSNLHAHKLRVNPVNFKLLSHSLLVTLASHLPTNFTPAVHANLNKFLANDSTVLTSKYR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 


Chain B from PDB  Type:PROTEIN  Length:145
 aligned with HBB_ODOVI | P02074 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     
            HBB_ODOVI     1 MLTAEEKAAVTGFWGKVNVDVVGAEALGRLLVVYPWTQRFFEHFGDLSSAGAVMGNPKVKAHGKRVLDAFSEGLKHLDDLKGAFAELSELHCNKLHVDPENFRLLGNVLVVVLARNFGGEFTPLVQADFQKVVAGVANALAHRYH 145
               SCOP domains d1hdsb_ B: Hemoglobin, beta-chain                                                                                                                 SCOP domains
               CATH domains 1hdsB00 B:1-145 Globins                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh......hhhhhhhhhhh........hhhhh....hhhhhhhhhhhhhhhhhh...................hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -GLOBIN  PDB: B:2-145 UniProt: 2-145                                                                                                              PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hds B   1 MLTAEEKAAVTGFWGKVDVDVVGAQALGRLLVVYPWTQRFFQHFGNLSSAGAVMNNPKVKAHGKRVLDAFTQGLKHLDDLKGAFAQLSGLHCNKLHVNPQNFRLLGNVLALVVARNFGGQFTPNVQALFQKVVAGVANALAHKYH 145
                                    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_ODOVI | P01972 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 
            HBA_ODOVI     1 VLSAABKSBVKAAWGKVGGNAAPYGAZALZRMFLSFPTTKTYFPHFBLSHGSAZVKAHGZKVABALTKAVGHLBBLPGTLSBLSBLHAHKLRVBPVBFKLLSHSLLVTLATHLPBBFTPAVHASLBKFLABVSTVLTSKYR 141
               SCOP domains d1hdsc_ C: Hemoglobin, alpha-chain                                                                                                            SCOP domains
               CATH domains 1hdsC00 C:1-141 Globins                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----T--------------K---F--------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: C:2-141 UniProt: 2-141                                                                                                          PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hds C   1 VLSAANKSNVKAAWGKVGGNAPAYGAQALQRMFLSFPTTKTYFPHFDLSHGSAQQKAHGQKVANALTKAQGHLNDLPGTLSNLSNLHAHKLRVNPVNFKLLSHSLLVTLASHLPTNFTPAVHANLNKFLANDSTVLTSKYR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 


Chain D from PDB  Type:PROTEIN  Length:145
 aligned with HBB_ODOVI | P02074 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     
            HBB_ODOVI     1 MLTAEEKAAVTGFWGKVNVDVVGAEALGRLLVVYPWTQRFFEHFGDLSSAGAVMGNPKVKAHGKRVLDAFSEGLKHLDDLKGAFAELSELHCNKLHVDPENFRLLGNVLVVVLARNFGGEFTPLVQADFQKVVAGVANALAHRYH 145
               SCOP domains d1hdsd_ D: Hemoglobin, beta-chain                                                                                                                 SCOP domains
               CATH domains 1hdsD00 D:1-145 Globins                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh.......hhhhhh....hhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -GLOBIN  PDB: D:2-145 UniProt: 2-145                                                                                                              PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hds D   1 MLTAEEKAAVTGFWGKVDVDVVGAQALGRLLVVYPWTQRFFQHFGNLSSAGAVMNNPKVKAHGKRVLDAFTQGLKHLDDLKGAFAQLSGLHCNKLHVNPQNFRLLGNVLALVVARNFGGQFTPNVQALFQKVVAGVANALAHKYH 145
                                    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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HDS)

(-) Gene Ontology  (8, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (HBA_ODOVI | P01972)
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_ODOVI | P02074)
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

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