Interaction between Cytochrome c iso-1 (5cid_B) and Cytochrome c peroxidase, mitochondrial (5cid_C)

PDB and SCOP data

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

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

Release date: 2016-08-03

Resolution: 2.8 Å

  • Chain A: 5cid_B

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 108

  • Chain B: 5cid_C

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 298.46 Å2

Number of inter-residue contacts at the interface: 26

Number of salt bridges: 1

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 4 proteins.

    Download PDB coordinates


Create a structural model for this interaction

  • Interface residues in 5cid_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 -5 1 T 37.0 23.9 %
    2 -4 2 E 64.4 69.9 %
    3 -3 3 F 9.4 52.4 %
    4 -2 4 K 1.9 1.2 %
    5 62 67 N 9.2 11.8 %
    6 63 68 N 13.9 53.0 %
    7 66 71 E 64.6 71.2 %
    8 69 74 T 1.3 4.0 %
    9 73 78 K 1.4 0.8 %
    10 74 79 Y 18.8 24.3 %
    11 86 91 K 3.2 2.6 %
    12 87 92 K 12.3 8.6 %
    13 88 93 E 37.7 51.4 %
    14 89 94 K 14.9 9.6 %
    15 91 96 R 8.5 34.5 %

  • Interface residues in 5cid_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 21 21 K 0.9 0.7 %
    2 29 29 K 22.9 47.5 %
    3 32 32 E 15.5 13.9 %
    4 33 33 D 19.3 54.0 %
    5 35 35 E 16.8 17.9 %
    6 86 86 Q 3.7 5.2 %
    7 90 90 K 53.4 43.3 %
    8 93 93 E 26.8 24.3 %
    9 94 94 P 54.7 80.3 %
    10 97 97 K 72.7 46.3 %
    11 98 98 E 11.8 10.0 %

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 86 86 Q 3.7
2 -5 1 T 90 90 K 30.9
3 -5 1 T 93 93 E 2.4
4 -4 2 E 29 29 K 0.5
5 -4 2 E 90 90 K 22.5
6 -4 2 E 93 93 E 24.4
7 -4 2 E 94 94 P 17.0
8 -3 3 F 94 94 P 9.4
9 -2 4 K 35 35 E 1.9
10 62 67 N 97 97 K 9.2
11 63 68 N 97 97 K 13.9
12 66 71 E 94 94 P 23.8
13 66 71 E 97 97 K 30.9
14 66 71 E 98 98 E 10.0
15 69 74 T 98 98 E 1.3
16 73 78 K 21 21 K 0.9
17 73 78 K 98 98 E 0.5
18 74 79 Y 97 97 K 18.8
19 86 91 K 32 32 E 3.2
20 87 92 K 32 32 E 12.3
21 88 93 E 29 29 K 18.1 Salt bridge
22 88 93 E 33 33 D 19.3
23 88 93 E 94 94 P 0.4
24 89 94 K 35 35 E 14.9
25 91 96 R 29 29 K 4.3
26 91 96 R 94 94 P 4.2

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: 5cid_B; 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% (15/15).

    Identities = 100% (15/15), Positive = 100% (15/15), Gaps = 0% (0/15).

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    5cid_B: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

    dssp: -------HHHHHHHHHHH-------------------------E----------HHHHH-


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    5cid_B: 61 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 108

    dssp: --E--HHHHHHH---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: 5cid_C; 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% (11/11).

    Identities = 100% (11/11), Positive = 100% (11/11), Gaps = 0% (0/11).

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    5cid_C: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    5cid_C: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    5cid_C: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    5cid_C: 181 HLKNSGYEGPGGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    5cid_C: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

    dssp: -HHHHHHHHHHH--HHHHHHHHHHHHHHHHH--EE--------E----------


    Download alignment FASTA file