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(-) Description

Title :  M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH NICOTINAMIDE
 
Authors :  A. Pesce, L. Tilleman, J. Donne, E. Aste, P. Ascenzi, C. Ciaccio, M. Cole L. Moens, C. Viappiani, S. Dewilde, M. Bolognesi, M. Nardini
Date :  18 Jan 13  (Deposition) - 26 Jun 13  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Iron-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Pesce, L. Tilleman, J. Donne, E. Aste, P. Ascenzi, C. Ciaccio, M. Coletta, L. Moens, C. Viappiani, S. Dewilde, M. Bolognesi, M. Nardini
Structure And Haem-Distal Site Plasticity In Methanosarcina Acetivorans Protoglobin.
Plos One V. 8 66144 2013
PubMed-ID: 23776624  |  Reference-DOI: 10.1371/JOURNAL.PONE.0066144

(-) Compounds

Molecule 1 - PROTOGLOBIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: METHANOSARCINA ACETIVORANS
    Organism Taxid: 2214

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3NCA2Ligand/IonNICOTINAMIDE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:70 , TYR A:73 , PHE A:74 , TYR A:85 , VAL A:89 , ARG A:92 , PHE A:93 , TRP A:96 , TYR A:112 , ARG A:119 , HIS A:120 , LYS A:125 , ASN A:126 , ILE A:137 , TYR A:141 , PHE A:145 , ILE A:149 , VAL A:182 , TRP A:185 , NCA A:300 , HOH A:2089 , HOH A:2090 , HOH A:2119 , HOH A:2127BINDING SITE FOR RESIDUE HEM A 200
2AC2SOFTWARETRP A:60 , TYR A:61 , VAL A:64 , PHE A:74 , PHE A:93 , PHE A:145 , HEM A:200BINDING SITE FOR RESIDUE NCA A 300
3AC3SOFTWARELEU B:70 , TYR B:73 , PHE B:74 , TYR B:85 , VAL B:89 , ARG B:92 , PHE B:93 , TRP B:96 , TYR B:112 , ARG B:119 , HIS B:120 , LYS B:125 , ASN B:126 , ILE B:137 , TYR B:141 , PHE B:145 , ILE B:149 , VAL B:182 , TRP B:185 , NCA B:300 , HOH B:2092 , HOH B:2093 , HOH B:2123 , HOH B:2127BINDING SITE FOR RESIDUE HEM B 200
4AC4SOFTWARETRP B:60 , TYR B:61 , VAL B:64 , PHE B:74 , PHE B:93 , PHE B:145 , ILE B:149 , HEM B:200 , HOH B:2159BINDING SITE FOR RESIDUE NCA B 300
5AC5SOFTWARETYR A:9 , TYR A:11 , GLU A:13 , ARG A:95 , ARG A:103 , LEU B:22BINDING SITE FOR RESIDUE GOL A1196

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZJQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZJQ)

(-) 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:190
 aligned with Q8TLY9_METAC | Q8TLY9 from UniProtKB/TrEMBL  Length:195

    Alignment length:190
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195
         Q8TLY9_METAC     6 IPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTCNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zjq A   6 IPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195


Chain B from PDB  Type:PROTEIN  Length:191
 aligned with Q8TLY9_METAC | Q8TLY9 from UniProtKB/TrEMBL  Length:195

    Alignment length:191
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194 
         Q8TLY9_METAC     5 KIPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTCNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zjq B   5 KIPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 3ZJQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZJQ)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8TLY9_METAC | Q8TLY9)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    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).

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 Related Entries

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

UniProtKB/TrEMBL
        Q8TLY9_METAC | Q8TLY9: 2veb 2vee 3qzx 3qzz 3r0g 3zh0 3zjh 3zji 3zjj 3zjl 3zjm 3zjn 3zjo 3zjp 3zjr 3zjs 3zol 3zom

(-) Related Entries Specified in the PDB File

3zjh TRP(60)B9ALA MUTATION OF M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE
3zji TYR(61)B10ALA MUTATION OF M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE
3zjj PHE(93)E11LEU MUTATION OF M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE
3zjl LEU(142)G4ALA MUTATION OF M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE
3zjm ILE(149)G11PHE MUTATION OF M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE
3zjn M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE
3zjo M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH AZIDE
3zjp M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH IMIDAZOLE