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(-) Description

Title :  CRYSTAL STRUCTURE OF T-STATE CARBONMONOXY HEMOGLOBIN FROM TREMATOMUS BERNACCHII AT PH 8.4
 
Authors :  A. Merlino, A. Balsamo, L. Mazzarella, A. Vergara
Date :  15 Jan 13  (Deposition) - 20 Feb 13  (Release) - 23 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Globin Fold, Oxygen Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Ronda, A. Merlino, S. Bettati, C. Verde, A. Balsamo, L. Mazzarella, A. Mozzarelli, A. Vergara
Role Of Tertiary Structures On The Root Effect In Fish Hemoglobins.
Biochim. Biophys. Acta V. 1834 1885 2013
PubMed-ID: 23376186  |  Reference-DOI: 10.1016/J.BBAPAP.2013.01.031

(-) Compounds

Molecule 1 - HEMOGLOBIN SUBUNIT ALPHA
    Chains: A, C
    Organism Common: ROCKCOD
    Organism Scientific: TREMATOMUS BERNACCHII
    Organism Taxid: 40690
    Synonym: ALPHA-GLOBIN, HEMOGLOBIN ALPHA CHAIN
 
Molecule 2 - HEMOGLOBIN SUBUNIT BETA
    Chains: B, D
    Organism Common: ROCKCOD
    Organism Scientific: TREMATOMUS BERNACCHII
    Organism Taxid: 40690
    Synonym: BETA-GLOBIN, HEMOGLOBIN BETA CHAIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2CMO1Ligand/IonCARBON MONOXIDE
3HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:43 , HIS A:59 , VAL A:63 , HEM A:202BINDING SITE FOR RESIDUE CMO A 201
2AC2SOFTWAREHIS A:45 , HIS A:59 , LYS A:62 , VAL A:63 , LEU A:84 , GLN A:87 , HIS A:88 , LEU A:92 , ASN A:98 , PHE A:99 , ASN A:103 , CMO A:201BINDING SITE FOR RESIDUE HEM A 202
3AC3SOFTWARETHR B:38 , HIS B:41 , PHE B:42 , HIS B:63 , LYS B:66 , VAL B:67 , LEU B:88 , LEU B:91 , HIS B:92 , LEU B:96 , VAL B:98 , ASN B:102 , LEU B:141BINDING SITE FOR RESIDUE HEM B 400
4AC4SOFTWARETYR C:42 , HIS C:45 , TRP C:46 , HIS C:59 , LYS C:62 , VAL C:63 , GLY C:66 , ILE C:67 , LEU C:84 , GLN C:87 , HIS C:88 , LEU C:92 , ASN C:98 , PHE C:99 , LEU C:102BINDING SITE FOR RESIDUE HEM C 600
5AC5SOFTWARETHR D:38 , HIS D:41 , PHE D:42 , HIS D:63 , LYS D:66 , LEU D:71 , HIS D:92 , LEU D:96 , VAL D:98 , PHE D:103 , LEU D:141BINDING SITE FOR RESIDUE HEM D 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IRO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4IRO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IRO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IRO)

(-) Exons   (0, 0)

(no "Exon" information available for 4IRO)

(-) 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
                                                                                                                                                                               
               SCOP domains d4iroa_ A: Hemoglobin, alpha-chain                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iro A   0 xSLSDKDKAAVRALWSKIGKSADAIGNDALSRMIVVYPQTKTYFSHWPDVTPGSPHIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPANFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR 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
                                                                                                                                                                                  
               SCOP domains d4irob_ B: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iro B   1 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLIVYPWTQRHFSGFGNLYNAEAIIGNANVAAHGIKVLHGLDRGVKNMDNIAATYADLSTLHSEKLHVDPDNFKLLSDCITIVLAAKMGHAFTAETQGAFQKFLAVVVSALGKQYH 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      


Chain C from PDB  Type:PROTEIN  Length:143
                                                                                                                                                                               
               SCOP domains d4iroc_ C: Hemoglobin, alpha-chain                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iro C   0 xSLSDKDKAAVRALWSKIGKSADAIGNDALSRMIVVYPQTKTYFSHWPDVTPGSPHIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPANFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR 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
                                                                                                                                                                                  
               SCOP domains d4irod_ D: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iro D   1 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLIVYPWTQRHFSGFGNLYNAEAIIGNANVAAHGIKVLHGLDRGVKNMDNIAATYADLSTLHSEKLHVDPDNFKLLSDCITIVLAAKMGHAFTAETQGAFQKFLAVVVSALGKQYH 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  (0, 0)

(no "CATH Domain" information available for 4IRO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IRO)

(-) Gene Ontology  (8, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        HBA_TREBE | P80043: 1hbh 1pbx 1s5x 1s5y 2h8d 2h8f 2peg 3gkv 3gqg 4g51 4odc
        HBB_TREBE | P80044: 1hbh 1pbx 1s5x 1s5y 2h8d 2h8f 2peg 3gkv 3gqg 4g51 4odc

(-) Related Entries Specified in the PDB File

2h8d CRYSTAL STRUCTURE OF DEOXY HEMOGLOBIN FROM TREMATOMUS BERNACCHII AT PH 8.4
2h8f CRYSTAL STRUCTURE OF DEOXY HEMOGLOBIN FROM TREMATOMUS BERNACCHII AT PH 6.2
3d1k R/T INTERMEDIATE QUATERNARY STRUCTURE OF AN ANTARCTIC FISH HEMOGLOBIN IN AN ALPHA(CO)-BETA(PENTACOORDINATE) STATE
3gkv X-RAY STRUCTURE OF AN INTERMEDIATE ALONG THE OXIDATION PATHWAY OF TREMATOMUS BERNACCHII HEMOGLOBIN
4esa X-RAY STRUCTURE OF CARBONMONOXY HEMOGLOBIN OF ELEGINOPS MACLOVINUS