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(-) Description

Title :  A ZN-MEDIATED TETRAHEDRAL PROTEIN LATTICE CAGE ENCAPSULATING A MICROPEROXIDASE
 
Authors :  F. A. Tezcan, T. W. Ni
Date :  10 Mar 10  (Deposition) - 12 Jan 11  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D,E  (1x)
Biol. Unit 2:  A,B,C,D,E  (3x)
Keywords :  Four-Helix Bundle, Electron Transport, Heme, Metal-Binding, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. W. Ni, F. A. Tezcan
Structural Characterization Of A Microperoxidase Inside A Metal-Directed Protein Cage.
Angew. Chem. Int. Ed. Engl. V. 49 7014 2010
PubMed-ID: 20721993  |  Reference-DOI: 10.1002/ANIE.201001487

(-) Compounds

Molecule 1 - SOLUBLE CYTOCHROME B562
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CYBC
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: CYTOCHROME B-562
 
Molecule 2 - HEME-PEPTIDE FRAGMENT
    Chains: E
    Engineered: YES
    Other Details: TRYPTIC CLEAVAGE PRODUCT
    Synonym: HEME-PEPTIDE FRAGMENT
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): ABCDE
Biological Unit 2 (3x): ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric Unit (3, 19)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2HEM5Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3ZN10Ligand/IonZINC ION
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2HEM5Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 27)
No.NameCountTypeFull Name
1ACT12Ligand/IonACETATE ION
2HEM15Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3ZN-1Ligand/IonZINC ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:1 , ASP A:39 , HIS A:77 , HOH A:228BINDING SITE FOR RESIDUE ZN A 107
02AC2SOFTWAREGLU A:8 , ASP A:12 , GLU C:8 , ASP C:12BINDING SITE FOR RESIDUE ZN A 108
03AC3SOFTWAREHIS A:59 , HIS A:63 , ACT A:151 , HOH A:259BINDING SITE FOR RESIDUE ZN A 109
04AC4SOFTWAREGLU A:4 , MET A:7 , ASN A:11 , PRO A:45 , PRO A:46 , PHE A:61 , PHE A:65 , CYS A:98 , CYS A:101 , HIS A:102 , TYR A:105 , ARG A:106 , HOH A:221 , HOH A:224 , HOH A:229 , HOH A:292 , GLN C:103BINDING SITE FOR RESIDUE HEM A 150
05AC5SOFTWAREASP A:54 , HIS A:59 , ARG A:62 , HIS A:63 , CYS A:67 , ZN A:109 , HOH A:283BINDING SITE FOR RESIDUE ACT A 151
06AC6SOFTWAREALA B:1 , ASP B:39 , HOH B:220 , HIS D:77BINDING SITE FOR RESIDUE ZN B 107
07AC7SOFTWAREGLU B:8 , ASP B:12 , GLU D:8 , ASP D:12BINDING SITE FOR RESIDUE ZN B 108
08AC8SOFTWAREASP B:54 , HIS B:59 , HOH B:247 , HIS D:63 , ACT D:107BINDING SITE FOR RESIDUE ZN B 109
09AC9SOFTWAREHIS B:63 , ACT B:151 , ASP C:54 , HIS C:59BINDING SITE FOR RESIDUE ZN B 110
10BC1SOFTWAREHIS B:77 , ALA C:1 , ASP C:39 , HOH C:209BINDING SITE FOR RESIDUE ZN B 111
11BC2SOFTWAREGLU B:4 , MET B:7 , PRO B:45 , PRO B:46 , PHE B:61 , PHE B:65 , CYS B:98 , CYS B:101 , HIS B:102 , TYR B:105 , ARG B:106 , HOH B:293BINDING SITE FOR RESIDUE HEM B 150
12BC3SOFTWAREHIS B:63 , CYS B:67 , ZN B:110 , HOH B:202 , PRO C:53 , ASP C:54 , HIS C:59 , ARG C:62BINDING SITE FOR RESIDUE ACT B 151
13BC4SOFTWAREGLU C:4 , MET C:7 , ASN C:11 , PRO C:45 , PRO C:46 , PHE C:61 , PHE C:65 , CYS C:98 , CYS C:101 , HIS C:102 , ARG C:106 , HOH C:213 , HOH C:221 , HOH C:224 , HOH C:280 , HOH C:292BINDING SITE FOR RESIDUE HEM C 150
14BC5SOFTWAREPRO B:53 , ASP B:54 , HIS B:59 , ARG B:62 , ZN B:109 , HIS D:63 , CYS D:67BINDING SITE FOR RESIDUE ACT D 107
15BC6SOFTWAREHIS C:63 , ASP D:54 , HIS D:59 , ACT D:151BINDING SITE FOR RESIDUE ZN D 108
16BC7SOFTWAREHIS C:77 , ALA D:1 , ASP D:39 , HOH D:225BINDING SITE FOR RESIDUE ZN D 109
17BC8SOFTWAREHIS C:63 , CYS C:67 , PRO D:53 , ASP D:54 , HIS D:59 , ARG D:62 , ZN D:108BINDING SITE FOR RESIDUE ACT D 151
18BC9SOFTWAREGLU D:4 , MET D:7 , PRO D:45 , PRO D:46 , PHE D:61 , PHE D:65 , CYS D:98 , CYS D:101 , HIS D:102 , TYR D:105 , ARG D:106 , HOH D:213 , HOH D:233 , HOH D:274 , HOH D:298BINDING SITE FOR RESIDUE HEM D 150
19CC1SOFTWARETHR B:31 , ALA B:34 , ALA B:38 , TRP B:66 , HIS B:73 , ASN B:80 , ALA C:38 , ASP C:39 , TRP C:41 , THR E:97 , CYS E:98 , CYS E:101 , HIS E:102 , HOH E:202 , HOH E:204 , HOH E:205BINDING SITE FOR RESIDUE HEM E 150

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M4C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3M4C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M4C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M4C)

(-) Exons   (0, 0)

(no "Exon" information available for 3M4C)

(-) 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:106
 aligned with C562_ECOLX | P0ABE7 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:106
                                    32        42        52        62        72        82        92       102       112       122      
           C562_ECOLX    23 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKYR 128
               SCOP domains d3m4ca_ A: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3m4c A   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAADAWSATPPKLEDKSPDSPEMHDFRHGFWCLIGQIHAALHLANEGKVKEAQAAAEQLKTTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain B from PDB  Type:PROTEIN  Length:106
 aligned with C562_ECOLX | P0ABE7 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:106
                                    32        42        52        62        72        82        92       102       112       122      
           C562_ECOLX    23 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKYR 128
               SCOP domains d3m4cb_ B: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3m4c B   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAADAWSATPPKLEDKSPDSPEMHDFRHGFWCLIGQIHAALHLANEGKVKEAQAAAEQLKTTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain C from PDB  Type:PROTEIN  Length:106
 aligned with C562_ECOLX | P0ABE7 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:106
                                    32        42        52        62        72        82        92       102       112       122      
           C562_ECOLX    23 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKYR 128
               SCOP domains d3m4cc_ C: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3m4c C   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAADAWSATPPKLEDKSPDSPEMHDFRHGFWCLIGQIHAALHLANEGKVKEAQAAAEQLKTTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain D from PDB  Type:PROTEIN  Length:106
 aligned with C562_ECOLX | P0ABE7 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:106
                                    32        42        52        62        72        82        92       102       112       122      
           C562_ECOLX    23 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKYR 128
               SCOP domains d3m4cd_ D: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Cytochrom_B562-3m4cD01 D:1-106                                                                             Pfam domains (1)
           Pfam domains (2) Cytochrom_B562-3m4cD02 D:1-106                                                                             Pfam domains (2)
           Pfam domains (3) Cytochrom_B562-3m4cD03 D:1-106                                                                             Pfam domains (3)
           Pfam domains (4) Cytochrom_B562-3m4cD04 D:1-106                                                                             Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3m4c D   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAADAWSATPPKLEDKSPDSPEMHDFRHGFWCLIGQIHAALHLANEGKVKEAQAAAEQLKTTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain E from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 3m4c E  95 KTTCNACHQ 103
   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  (1, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M4C)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: Cytochrom_B562] (14)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (C562_ECOLX | P0ABE7)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    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.
biological process
    GO:0022900    electron transport chain    A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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  3m4c
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  C562_ECOLX | P0ABE7
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 Related Entries

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

UniProtKB/Swiss-Prot
        C562_ECOLX | P0ABE7: 1apc 1lm3 1m6t 1qpu 1qq3 256b 2bc5 2qla 3c62 3c63 3de8 3de9 3foo 3fop 3hni 3hnj 3hnk 3hnl 3iq5 3iq6 3l1m 3m15 3m4b 3m79 3nmi 3nmj 3nmk 3tol 3tom 3u8p 4ea3 4eiy 4iaq 4iar 4ib4 4je9 4jea 4jeb 4jkv 4l6r 4n6h 4nc3 4ntj 4o9r 4or2 4pxz 4py0 4qim 4qin 4rwa 4rwd 4u9d 4u9e 4yay 4z34 4z35 4z36 4zud 5awi 5bu7 5dhg 5dhh 5iu4 5iu7 5iu8 5iua 5iub 5jtb 5k2a 5k2b 5k2c 5k2d 5l31 5l32 5l7d 5l7i 5ndd 5ndz 5nj6 5tvn 5uen 5uig 5unf 5ung 5unh 5uvi

(-) Related Entries Specified in the PDB File

256b 2qla 3m15 3m4b