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(-) Description

Title :  MET-PERCH HEMOGLOBIN AT 1.9A
 
Authors :  Center For Eukaryotic Structural Genomics (Cesg)
Date :  11 Oct 04  (Deposition) - 16 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Fish Hemoglobin, Rapid Oxidation, Structural Genomics, Protein Structure Initiative, Psi, Cesg, Center For Eukaryotic Structural Genomics, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Center For Eukaryotic Structural Genomics (Cesg)
Met-Perch Hemoglobin At 1. 9A
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOGLOBIN ALPHA-1 CHAIN
    Chains: A, C
    Organism Common: YELLOW PERCH
    Organism Scientific: PERCA FLAVESCENS
    Organism Taxid: 8167
 
Molecule 2 - HEMOGLOBIN BETA-2 CHAIN
    Chains: B, D
    Organism Common: YELLOW PERCH
    Organism Scientific: PERCA FLAVESCENS
    Organism Taxid: 8167

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

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

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:42 , PHE A:43 , HIS A:59 , THR A:62 , ILE A:63 , LEU A:84 , HIS A:88 , LEU A:92 , ASN A:98 , HOH A:378BINDING SITE FOR RESIDUE HEM A 143
2AC2SOFTWARETYR B:41 , PHE B:42 , HIS B:63 , LEU B:91 , HIS B:92 , LEU B:96 , ASN B:102 , LEU B:141 , HOH B:300 , HOH B:379BINDING SITE FOR RESIDUE HEM B 148
3AC3SOFTWARETYR C:42 , PHE C:43 , HIS C:45 , HIS C:59 , THR C:62 , LEU C:84 , LEU C:87 , HIS C:88 , LEU C:92 , ASN C:98 , LEU C:102 , LEU C:137 , HOH C:380BINDING SITE FOR RESIDUE HEM C 143
4AC4SOFTWARETYR D:41 , HIS D:63 , LEU D:88 , HIS D:92 , LEU D:96 , ASN D:102 , LEU D:106 , LEU D:141 , HOH D:199BINDING SITE FOR RESIDUE HEM D 148

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XQ5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XQ5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XQ5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XQ5)

(-) Exons   (0, 0)

(no "Exon" information available for 1XQ5)

(-) 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:143
 aligned with A8HTG8_PERFV | A8HTG8 from UniProtKB/TrEMBL  Length:143

    Alignment length:143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   
         A8HTG8_PERFV     1 MSLSAKDKDTVKLFWAKVADKAEEIGSDALSRMLAVYPQTKTYFSHWKDLSPGSAPVNKHGKTIMLGVADAVASIDDLNAGLLALSELHAFTLRVDPANFKILAHCILVVLSIKFPKDFTPEVHVSLDKFLAALARALSEKYR 143
               SCOP domains d1xq5a_ A: Hemoglobin, alpha-chain                                                                                                              SCOP domains
               CATH domains -1xq5A00 A:1-142 Globins                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xq5 A   0 xSLSSKDKDTVKALWGKIADKAEEIGSDALSRMLAVYPQTKTYFSHWKDLSPGSAPVNKHGKTIMGGIVDAVASIDDLNAGLLALSELHAFTLRVDPANFKILSHCILVLLAVKFPKDFTPEVHISYDKFFSALARALAEKYR 142
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139   
                            |                                                                                                                                              
                            0-ACE                                                                                                                                          


Chain A from PDB  Type:PROTEIN  Length:143
 aligned with D0VWV2_PERFV | D0VWV2 from UniProtKB/TrEMBL  Length:143

    Alignment length:143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   
         D0VWV2_PERFV     1 XSLSSKDKDTVKALWGKIADKAEEIGSDALSRMLAVYPQTKTYFSHWKDLSPGSAPVNKHGKTIMGGIVDAVASIDDLNAGLLALSELHAFTLRVDPANFKILSHCILVLLAVKFPKDFTPEVHISYDKFFSALARALAEKYR 143
               SCOP domains d1xq5a_ A: Hemoglobin, alpha-chain                                                                                                              SCOP domains
               CATH domains -1xq5A00 A:1-142 Globins                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xq5 A   0 xSLSSKDKDTVKALWGKIADKAEEIGSDALSRMLAVYPQTKTYFSHWKDLSPGSAPVNKHGKTIMGGIVDAVASIDDLNAGLLALSELHAFTLRVDPANFKILSHCILVLLAVKFPKDFTPEVHISYDKFFSALARALAEKYR 142
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139   
                            0-ACE                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:146
 aligned with D0VWV3_PERFV | D0VWV3 from UniProtKB/TrEMBL  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
         D0VWV3_PERFV     1 VVWTDFERATIADIFSKLDYEAVGGATLARCLIVYPWTQRYFGNFGNLYNAAAIMGNPMIAKHGTTILHGLDRAVKNMDNIKATYAELSVLHSEKLHVDPDNFKLLSDCLTIVVAAQLGKAFSGEVQAAFQKFLSVVVSALGKQYH 146
               SCOP domains d1xq5b_ B: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 1xq5B00 B:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xq5 B   1 VVWTDFERATIADIFSKLDYEAVGGATLARCLIVYPWTQRYFGNFGNLYNAAAIMGNPMIAKHGTTILHGLDRAVKNMDNIKATYAELSVLHSEKLHVDPDNFKLLSDCLTIVVAAQLGKAFSGEVQAAFQKFLSVVVSALGKQYH 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      


Chain C from PDB  Type:PROTEIN  Length:143
 aligned with A8HTG8_PERFV | A8HTG8 from UniProtKB/TrEMBL  Length:143

    Alignment length:143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   
         A8HTG8_PERFV     1 MSLSAKDKDTVKLFWAKVADKAEEIGSDALSRMLAVYPQTKTYFSHWKDLSPGSAPVNKHGKTIMLGVADAVASIDDLNAGLLALSELHAFTLRVDPANFKILAHCILVVLSIKFPKDFTPEVHVSLDKFLAALARALSEKYR 143
               SCOP domains d1xq5c_ C: Hemoglobin, alpha-chain                                                                                                              SCOP domains
               CATH domains -1xq5C00 C:1-142 Globins                                                                                                                        CATH domains
           Pfam domains (1) ------Globin-1xq5C01 C:6-107                                                                                ----------------------------------- Pfam domains (1)
           Pfam domains (2) ------Globin-1xq5C02 C:6-107                                                                                ----------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xq5 C   0 xSLSSKDKDTVKALWGKIADKAEEIGSDALSRMLAVYPQTKTYFSHWKDLSPGSAPVNKHGKTIMGGIVDAVASIDDLNAGLLALSELHAFTLRVDPANFKILSHCILVLLAVKFPKDFTPEVHISYDKFFSALARALAEKYR 142
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139   
                            0-ACE                                                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:143
 aligned with D0VWV2_PERFV | D0VWV2 from UniProtKB/TrEMBL  Length:143

    Alignment length:143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   
         D0VWV2_PERFV     1 XSLSSKDKDTVKALWGKIADKAEEIGSDALSRMLAVYPQTKTYFSHWKDLSPGSAPVNKHGKTIMGGIVDAVASIDDLNAGLLALSELHAFTLRVDPANFKILSHCILVLLAVKFPKDFTPEVHISYDKFFSALARALAEKYR 143
               SCOP domains d1xq5c_ C: Hemoglobin, alpha-chain                                                                                                              SCOP domains
               CATH domains -1xq5C00 C:1-142 Globins                                                                                                                        CATH domains
           Pfam domains (1) ------Globin-1xq5C01 C:6-107                                                                                ----------------------------------- Pfam domains (1)
           Pfam domains (2) ------Globin-1xq5C02 C:6-107                                                                                ----------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xq5 C   0 xSLSSKDKDTVKALWGKIADKAEEIGSDALSRMLAVYPQTKTYFSHWKDLSPGSAPVNKHGKTIMGGIVDAVASIDDLNAGLLALSELHAFTLRVDPANFKILSHCILVLLAVKFPKDFTPEVHISYDKFFSALARALAEKYR 142
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139   
                            0-ACE                                                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:146
 aligned with D0VWV3_PERFV | D0VWV3 from UniProtKB/TrEMBL  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
         D0VWV3_PERFV     1 VVWTDFERATIADIFSKLDYEAVGGATLARCLIVYPWTQRYFGNFGNLYNAAAIMGNPMIAKHGTTILHGLDRAVKNMDNIKATYAELSVLHSEKLHVDPDNFKLLSDCLTIVVAAQLGKAFSGEVQAAFQKFLSVVVSALGKQYH 146
               SCOP domains d1xq5d_ D: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 1xq5D00 D:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xq5 D   1 VVWTDFERATIADIFSKLDYEAVGGATLARCLIVYPWTQRYFGNFGNLYNAAAIMGNPMIAKHGTTILHGLDRAVKNMDNIKATYAELSVLHSEKLHVDPDNFKLLSDCLTIVVAAQLGKAFSGEVQAAFQKFLSVVVSALGKQYH 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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (8, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (D0VWV2_PERFV | D0VWV2)
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 A,C   (A8HTG8_PERFV | A8HTG8)
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   (D0VWV3_PERFV | D0VWV3)
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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  1xq5
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  A8HTG8_PERFV | A8HTG8
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  D0VWV2_PERFV | D0VWV2
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  D0VWV3_PERFV | D0VWV3
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        D0VWV3_PERFV | D0VWV3: 3bj1 3bj2 3bj3

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1XQ5)