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(-) Description

Title :  CRYSTAL STRUCTURE OF A DOMAIN-SWAPPED DIMER OF YEAST ISO-1-CYTOCHROME C WITH OMEGA-UNDECYLENYL-BETA-D-MALTOPYRANOSIDE
 
Authors :  B. E. Bowler, F. G. Whitby
Date :  25 Jun 16  (Deposition) - 22 Mar 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Electron Transport Apoptosis Lipid Binding, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Mcclelland, H. B. Steele, F. G. Whitby, T. C. Mou, D. Holley, J. B. Ross, S. R. Sprang, B. E. Bowler
Cytochrome C Can Form A Well-Defined Binding Pocket For Hydrocarbons.
J. Am. Chem. Soc. V. 138 16770 2016
PubMed-ID: 27990813  |  Reference-DOI: 10.1021/JACS.6B10745

(-) Compounds

Molecule 1 - CYTOCHROME C ISO-1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CYC1, YJR048W, J1653
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
16UZ2Ligand/IonOMEGA-UNDECYLENYL-BETA-D-MALTOPYRANOSIDE
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3SO44Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:13 , CYS A:14 , CYS A:17 , HIS A:18 , VAL A:28 , ILE A:35 , SER A:40 , GLY A:41 , TYR A:46 , TYR A:48 , THR A:49 , TRP A:59 , TYR A:67 , 6UZ A:202 , HOH A:305 , HOH A:306 , HOH A:309 , HOH A:310 , HOH A:312 , HOH A:317 , PHE B:82 , GLY B:83 , LEU B:94binding site for residue HEM A 201
2AC2SOFTWAREGLY A:1 , LYS A:55 , ASN A:62 , ASN A:63 , GLU A:66 , HEM A:201 , HOH A:303 , ASN B:92 , ILE B:95 , THR B:96binding site for residue 6UZ A 202
3AC3SOFTWARESER A:2 , ALA A:3 , LYS A:4 , SER A:47 , HOH A:327binding site for residue SO4 A 203
4AC4SOFTWARELYS A:4 , ALA A:43 , GLU A:44 , GLY A:45 , HOH A:313binding site for residue SO4 A 204
5AC5SOFTWAREPRO A:76 , GLY A:77 , THR A:78 , LYS A:79 , MET A:80 , LYS A:86binding site for residue SO4 A 205
6AC6SOFTWARELYS B:55 , TRP B:59 , GLU B:66 , TYR B:74 , HEM B:201binding site for residue 6UZ B 202
7AC7SOFTWARELYS B:86 , LYS B:87 , GLU B:88 , HOH B:303binding site for residue SO4 B 203
8AC8SOFTWAREALA A:81 , PHE A:82 , GLY A:83 , LEU A:85 , ARG B:13 , CYS B:14 , LEU B:15 , GLN B:16 , HIS B:18 , LYS B:27 , VAL B:28 , GLY B:29 , PRO B:30 , ILE B:35 , SER B:40 , GLY B:41 , TYR B:48 , THR B:49 , TRP B:59 , TYR B:67 , 6UZ B:202 , HOH B:306binding site for Di-peptide HEM B 201 and CYS B 17
9AC9SOFTWAREALA A:81 , PHE A:82 , GLY A:83 , LEU A:85 , PHE B:10 , ARG B:13 , LEU B:15 , GLN B:16 , CYS B:17 , HIS B:18 , VAL B:28 , GLY B:29 , PRO B:30 , ILE B:35 , SER B:40 , GLY B:41 , TYR B:48 , THR B:49 , TRP B:59 , TYR B:67 , 6UZ B:202 , HOH B:306binding site for Di-peptide HEM B 201 and CYS B 14

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KLU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5KLU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KLU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KLU)

(-) Exons   (0, 0)

(no "Exon" information available for 5KLU)

(-) 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:103
                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...................................hhhhhh....hhhhhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 5klu A   1 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPAKYIPGTKMAFGGLKKEKDRNDLITYLKKASE 103
                                    10        20        30        40        50        60        70        80        90       100   


Chain B from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh...............................................hhhhhhh.hhhhhh...hhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 5klu B  -3 FKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPAKYIPGTKMAFGGLKKEKDRNDLITYLKKASE 103
                              ||     7        17        27        37        47        57        67        77        87        97      
                             -1|                                                                                                      
                               1
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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 5KLU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KLU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KLU)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  5klu
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  CYC1_YEAST | P00044
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 Related Entries

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

UniProtKB/Swiss-Prot
        CYC1_YEAST | P00044: 1chh 1chi 1chj 1cie 1cif 1cig 1cih 1crg 1crh 1cri 1crj 1csu 1csv 1csw 1csx 1cty 1ctz 1fhb 1irv 1irw 1kyo 1lms 1nmi 1rap 1raq 1s6v 1u74 1ycc 1yfc 1yic 2b0z 2b10 2b11 2b12 2bcn 2gb8 2hv4 2jqr 2jti 2lir 2lit 2mhm 2n18 2orl 2pcc 2ycc 3cx5 3tyi 4mu8 4n0k 4p4q 4q5p 4qao 4ye1 5cib 5cic 5cid 5cie 5cif 5cig 5cih 5kke 5kpf 5lft 5lyc 5t7h

(-) Related Entries Specified in the PDB File

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