Interaction between Cytochrome c iso-1 (5cic_D) and Cytochrome c peroxidase, mitochondrial (5cic_A)

PDB and SCOP data

PDB ID: 5cic (all binary interactions in this PDB entry)

Title: Complex of yeast cytochrome c peroxidase (W191G) bound to 3-aminobenzotrifluoride with iso-1 cytochrome c

Release date: 2016-08-03

Resolution: 2.1 Å

  • Chain A: 5cic_D

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 108

  • Chain B: 5cic_A

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 201.45 Å2

Number of inter-residue contacts at the interface: 15

Number of salt bridges: 2

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 4 proteins.

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Create a structural model for this interaction

  • Interface residues in 5cic_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 -5 1 T 6.4 4.4 %
    2 -4 2 E 68.2 41.8 %
    3 62 67 N 20.5 29.9 %
    4 63 68 N 3.9 15.3 %
    5 66 71 E 26.5 27.5 %
    6 73 78 K 15.6 9.8 %
    7 86 91 K 0.9 0.7 %
    8 87 92 K 25.5 17.7 %
    9 88 93 E 34.0 31.8 %

  • Interface residues in 5cic_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 29 29 K 15.5 32.0 %
    2 32 32 E 31.5 24.0 %
    3 33 33 D 10.9 32.9 %
    4 90 90 K 6.4 5.0 %
    5 93 93 E 37.1 43.4 %
    6 94 94 P 14.7 21.0 %
    7 97 97 K 69.8 42.9 %
    8 98 98 E 15.6 13.9 %

No. Residue no. in chain A structure Residue no. in chain A sequence Residue in chain A Residue no. in chain B structure Residue no. in chain B sequence Residue in chain B Contact area, Å2 Contact type
1 -5 1 T 90 90 K 6.4
2 -4 2 E 90 90 K <0.1
3 -4 2 E 93 93 E 37.1
4 -4 2 E 94 94 P 12.2
5 -4 2 E 97 97 K 18.9
6 62 67 N 97 97 K 20.5
7 63 68 N 97 97 K 3.9
8 66 71 E 97 97 K 26.5 Salt bridge
9 73 78 K 98 98 E 15.6
10 86 91 K 32 32 E 0.9
11 87 92 K 32 32 E 25.5
12 88 93 E 29 29 K 15.5 Salt bridge
13 88 93 E 32 32 E 5.1
14 88 93 E 33 33 D 10.9
15 88 93 E 94 94 P 2.5

Analyse interface in VoroContacts server

  • Query protein: sp|P00044|CYC1_YEAST Cytochrome c iso-1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CYC1 PE=1 SV=2

    Result domain: 5cic_D; Cytochrome c iso-1

    Alignment data:

    Expectation value = 1.54e-77, Score = 226 bits (575),

    Identities = 100% (108/108), Positive = 100% (108/108), Gaps = 0% (0/108).

    Interface alignment data:

    Interface residues in alignment: 100% (9/9).

    Identities = 100% (9/9), Positive = 100% (9/9), Gaps = 0% (0/9).

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    5cic_D: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

    dssp: -------HHHHHHHHHHH-------------------------E----------HHHHHH


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    5cic_D: 61 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 108

    dssp: --E--HHHHHHHHH-HHHH-------------HHHHHHHHHHHHHH--


    Download alignment FASTA file

  • Query protein: sp|P00431|CCPR_YEAST Cytochrome c peroxidase, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CCP1 PE=1 SV=2

    Result domain: 5cic_A; Cytochrome c peroxidase, mitochondrial

    Alignment data:

    Expectation value = 0, Score = 607 bits (1564),

    Identities = 99% (291/294), Positive = 99% (291/294), Gaps = 0% (0/294).

    Interface alignment data:

    Interface residues in alignment: 100% (8/8).

    Identities = 100% (8/8), Positive = 100% (8/8), Gaps = 0% (0/8).

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    5cic_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

    dssp: -----EE--------HHHHHHHHHHHHHHHHH---HHHH---HHHHHHHHHHHH---E--


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    5cic_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

    dssp: --E------HHH-HHHH--HHH---HHHHHHHHHHHHH-----HHHHHHHHHHHHHHH--


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    5cic_A: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

    dssp: -----E--------HHH-------------HHHHHHHHH-----HHHHHHHHHHHH--EE


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    5cic_A: 181 HLKNSGYEGPGGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

    dssp: -HHHH---EE----------HHHHHHHH--EEEEE-----EEEEE----EE-HHHHHHHH


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    5cic_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

    dssp: -HHHHHHHHHHHH-HHHHHHHHHHHHHHHHH--EE--------E-----HHH--


    Download alignment FASTA file