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(-) Description

Title :  CRYSTAL STRUCTURE OF TREMATOMUS BERNACCHII HEMOGLOBIN IN A PARTIALLY CYANIDED STATE
 
Authors :  L. Mazzarella, A. Merlino, L. Vitagliano, A. Vergara
Date :  10 Jan 14  (Deposition) - 24 Dec 14  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Alpha Protein, Globin Fold, Oxygen Transport, Oxygen Transport- Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Mazzarella, A. Merlino, L. Vitagliano, C. Verde, G. Di Prisco, J. Peisach, A. Vergara
Structural Modifications Induced By The Switch From An Endogenous Bis-Histidyl To An Exogenous Cyanomet Hexa-Coordination In A Tetrameric Haemoglobin
Rsc Adv V. 4 25852 2014
PubMed: search

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB
Biological Unit 2 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2CYN2Ligand/IonCYANIDE ION
3GOL1Ligand/IonGLYCEROL
4HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (4, 12)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2CYN4Ligand/IonCYANIDE ION
3GOL2Ligand/IonGLYCEROL
4HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (4, 6)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2CYN2Ligand/IonCYANIDE ION
3GOL1Ligand/IonGLYCEROL
4HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:30 , HIS A:60 , VAL A:64 , HOH A:201 , HEM A:203BINDING SITE FOR RESIDUE CYN A 202
2AC2SOFTWARETYR A:43 , HIS A:46 , TRP A:47 , HIS A:60 , LYS A:63 , GLN A:88 , HIS A:89 , LEU A:93 , VAL A:95 , ASN A:99 , PHE A:100 , LEU A:103 , ASN A:104 , LEU A:138 , HOH A:201 , CYN A:202 , HOH A:1057 , HOH A:1074 , HOH A:1147 , ASN B:47BINDING SITE FOR RESIDUE HEM A 203
3AC3SOFTWAREHIS B:63 , VAL B:67 , HEM B:202BINDING SITE FOR RESIDUE CYN B 201
4AC4SOFTWAREHIS B:41 , PHE B:42 , HIS B:63 , LYS B:66 , HIS B:92 , LEU B:96 , ASN B:102 , PHE B:103 , LEU B:106 , LEU B:141 , CYN B:201 , HOH B:477BINDING SITE FOR RESIDUE HEM B 202
5AC5SOFTWAREVAL B:1 , MET B:78 , ASP B:79 , ASN B:80 , ILE B:81 , ALA B:82 , HIS B:146BINDING SITE FOR RESIDUE GOL B 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ODC)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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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 ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4odc A   1 xSLSDKDKAAVRALWSKIGKSADAIGNDALSRMIVVYPQTKTYFSHWPDVTPGSPHIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPANFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR 143
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140   
                            |                                                                                                                                              
                            1-ACE                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:146
                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4odc B   1 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLIVYPWTQRHFSGFGNLYNAEAIIGNANVAAHGIKVLHGLDRGVKNMDNIAATYADLSTLHSEKLHVDPDNFKLLSDCITIVLAAKMGHAFTAETQGAFQKFLAVVVSALGKQYH 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4ODC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 16)

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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 4iro
        HBB_TREBE | P80044: 1hbh 1pbx 1s5x 1s5y 2h8d 2h8f 2peg 3gkv 3gqg 4g51 4iro

(-) Related Entries Specified in the PDB File

1la6 CRYSTAL STRUCTURE OF TETRAMERIC HEMOGLOBIN IN A PARTIAL HEMICHROME STATE
1s5x CRYSTAL STRUCTURE OF TREMATOMUS BERNACCHII HEMOGLOBIN OXIDIZED BY AIR
1s5y CRYSTAL STRUCTURE OF TREMATOMUS BERNACCHII HEMOGLOBIN OXIDIZED BY FERRICYANIDE
2peg CRYSTAL STRUCTURE OF TREMATOMUS BERNACCHII HEMOGLOBIN IN A PARTIAL HEMICHROME STATE