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(-) Description

Title :  M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH IMIDAZOLE
 
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 :  1.38
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
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
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: METHANOSARCINA ACETIVORANS
    Organism Taxid: 2214

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3IMD1Ligand/IonIMIDAZOLE
4PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (4, 18)
No.NameCountTypeFull Name
1GOL10Ligand/IonGLYCEROL
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3IMD2Ligand/IonIMIDAZOLE
4PO44Ligand/IonPHOSPHATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
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 , LEU A:142 , PHE A:145 , VAL A:182 , TRP A:185 , IMD A:449 , HOH A:2167 , HOH A:2168 , HOH A:2200 , HOH A:2208BINDING SITE FOR RESIDUE HEM A 200
2AC2SOFTWAREGLY A:12 , GLU A:13 , THR A:14 , GLU A:15 , ASN A:16 , ALA A:108 , ASP A:111 , HOH A:2019BINDING SITE FOR RESIDUE PO4 A 201
3AC3SOFTWARETYR A:72 , VAL A:134 , PRO A:135 , ASN A:136 , GOL A:204 , HOH A:2135 , HOH A:2253 , HOH A:2254BINDING SITE FOR RESIDUE PO4 A 202
4AC4SOFTWAREGLU A:13 , ASN A:21 , LEU A:22 , GLU A:23 , GLN A:107BINDING SITE FOR RESIDUE GOL A 203
5AC5SOFTWARESER A:66 , ARG A:122 , PRO A:135 , PO4 A:202 , HOH A:2121 , HOH A:2124 , HOH A:2251 , HOH A:2254BINDING SITE FOR RESIDUE GOL A 204
6AC6SOFTWARELEU A:27 , ARG A:140 , TYR A:141 , HOH A:2128 , HOH A:2222 , HOH A:2253 , HOH A:2256BINDING SITE FOR RESIDUE GOL A 205
7AC7SOFTWAREPRO A:164 , GLU A:165 , TYR A:187 , PRO A:188 , VAL A:190 , LYS A:191 , TYR A:192 , HOH A:2257BINDING SITE FOR RESIDUE GOL A 206
8AC8SOFTWAREGLU A:30 , HIS A:67 , PRO A:68 , HIS A:69 , HOH A:2064BINDING SITE FOR RESIDUE GOL A 207
9AC9SOFTWARETRP A:60 , TYR A:61 , PHE A:93 , HEM A:200BINDING SITE FOR RESIDUE IMD A 449

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ZJP)

(-) Sequences/Alignments

Asymmetric 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: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....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zjp A   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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  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 3ZJP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (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 3zjq 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
3zjq M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH NICOTINAMIDE
3zjr M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE AND XENON
3zjs M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH AZIDE AND XENON