Interaction between Cytochrome c iso-1 (5cib_B) and Cytochrome c peroxidase, mitochondrial (5cib_C)

PDB and SCOP data

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

Title: Complex of yeast cytochrome c peroxidase (W191G) bound to 2,4-dimethylaniline with iso-1 cytochrome c

Release date: 2016-08-03

Resolution: 3.0 Å

  • Chain A: 5cib_B

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 108

  • Chain B: 5cib_C

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 355.34 Å2

Number of inter-residue contacts at the interface: 26

Number of H-bonds: 1

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 5cib_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 -5 1 T 1.4 1.0 %
    2 -4 2 E 69.9 44.1 %
    3 -2 4 K 25.1 16.6 %
    4 62 67 N 17.5 23.0 %
    5 63 68 N 1.2 6.0 %
    6 66 71 E 41.0 45.2 %
    7 69 74 T 18.1 50.9 %
    8 73 78 K 11.2 7.2 %
    9 86 91 K 19.4 15.2 %
    10 87 92 K 31.9 27.0 %
    11 88 93 E 54.5 56.9 %
    12 89 94 K 45.4 37.3 %
    13 91 96 R 18.7 50.2 %

  • Interface residues in 5cib_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 28 28 L 5.2 7.4 %
    2 29 29 K 21.4 46.9 %
    3 32 32 E 64.1 58.3 %
    4 33 33 D 29.7 59.1 %
    5 35 35 E 20.1 15.3 %
    6 86 86 Q 7.7 6.3 %
    7 89 89 F 0.8 1.8 %
    8 90 90 K 66.7 63.1 %
    9 93 93 E 24.9 38.3 %
    10 94 94 P 20.5 44.2 %
    11 97 97 K 62.4 43.0 %
    12 98 98 E 32.1 29.1 %

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 1.4
2 -4 2 E 86 86 Q 7.7
3 -4 2 E 89 89 F 0.8
4 -4 2 E 90 90 K 33.8
5 -4 2 E 93 93 E 24.9
6 -4 2 E 97 97 K 2.7
7 -2 4 K 90 90 K 25.1
8 62 67 N 97 97 K 17.5
9 63 68 N 97 97 K 1.2
10 66 71 E 97 97 K 41.0
11 69 74 T 98 98 E 18.1
12 73 78 K 98 98 E 11.2
13 86 91 K 28 28 L 5.2
14 86 91 K 32 32 E 14.3
15 87 92 K 32 32 E 31.9 Salt bridge
16 88 93 E 29 29 K 17.8 H-bond, Salt bridge
17 88 93 E 32 32 E 1.3
18 88 93 E 33 33 D 20.9
19 88 93 E 90 90 K 6.4
20 88 93 E 94 94 P 8.1
21 89 94 K 32 32 E 16.6
22 89 94 K 33 33 D 8.8
23 89 94 K 35 35 E 20.1
24 91 96 R 29 29 K 3.6
25 91 96 R 94 94 P 12.3
26 91 96 R 98 98 E 2.8

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: 5cib_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% (13/13).

    Identities = 100% (13/13), Positive = 100% (13/13), Gaps = 0% (0/13).

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    5cib_B: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

    dssp: ------------HHHHHH-------------------------E----------HHHHH-


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    5cib_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: 5cib_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% (12/12).

    Identities = 100% (12/12), Positive = 100% (12/12), Gaps = 0% (0/12).

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    5cib_C: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    5cib_C: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

    dssp: --E------HHH-------------HHHHH--HHHHHH-----HHHHHHHHHHHHHHH--


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    5cib_C: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

    dssp: -----E------------------------HHHHHHHH------HHHHHHHHHHHH---E


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    5cib_C: 181 HLKNSGYEGPGGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

    dssp: --------E-----------HHHHHHHH---EEEE-----EEEE-----EE-HHHHHHHH


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    5cib_C: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file