Interaction between Cytochrome c iso-1 (5cie_B) and Cytochrome c peroxidase, mitochondrial (5cie_C)

PDB and SCOP data

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

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

Release date: 2016-08-03

Resolution: 2.6 Å

  • Chain A: 5cie_B

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 108

  • Chain B: 5cie_C

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 293.81 Å2

Number of inter-residue contacts at the interface: 21

Number of salt bridges: 1

  • 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 5cie_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 -5 1 T 4.7 3.9 %
    2 -4 2 E 81.6 56.0 %
    3 62 67 N 10.4 16.0 %
    4 66 71 E 42.6 47.0 %
    5 69 74 T 1.3 3.2 %
    6 73 78 K 41.7 27.4 %
    7 86 91 K 15.5 11.9 %
    8 87 92 K 29.3 22.0 %
    9 88 93 E 36.7 45.8 %
    10 89 94 K 23.4 18.2 %
    11 91 96 R 6.7 23.1 %

  • Interface residues in 5cie_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 28 28 L 1.0 1.1 %
    2 29 29 K 9.6 23.0 %
    3 32 32 E 45.8 44.2 %
    4 33 33 D 19.8 37.3 %
    5 35 35 E 23.4 20.0 %
    6 90 90 K 33.4 26.0 %
    7 93 93 E 26.3 47.2 %
    8 94 94 P 24.7 39.8 %
    9 97 97 K 66.8 42.3 %
    10 98 98 E 41.8 38.6 %
    11 99 99 F 0.8 4.3 %
    12 100 100 P 0.4 0.4 %

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 4.7
2 -4 2 E 90 90 K 28.6
3 -4 2 E 93 93 E 26.3
4 -4 2 E 94 94 P 12.8
5 -4 2 E 97 97 K 13.9
6 62 67 N 97 97 K 10.4
7 66 71 E 97 97 K 42.5
8 66 71 E 98 98 E <0.1
9 69 74 T 98 98 E 1.3
10 73 78 K 98 98 E 40.5
11 73 78 K 99 99 F 0.8
12 73 78 K 100 100 P 0.4
13 86 91 K 28 28 L 1.0
14 86 91 K 32 32 E 14.5
15 87 92 K 32 32 E 29.3 Salt bridge
16 88 93 E 29 29 K 9.6
17 88 93 E 32 32 E 2.0
18 88 93 E 33 33 D 19.8
19 88 93 E 94 94 P 5.2
20 89 94 K 35 35 E 23.4
21 91 96 R 94 94 P 6.7

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: 5cie_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% (11/11).

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

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    5cie_B: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

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


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    5cie_B: 61 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 108

    dssp: -----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: 5cie_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

    5cie_C: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    5cie_C: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

    dssp: --E-----------HHHH-------HHHHHHHHHHHH------HHHHHHHHHHHHHHH--


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    5cie_C: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    5cie_C: 181 HLKNSGYEGPGGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

    dssp: -HHHH---EE----------HHHHHHHH---EEEE-----EEEE-----EE-HHHH----


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    5cie_C: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

    dssp: -HHHHHHHHHHHH-HHHHHHHHHHHHHHHH---EE--------E-----HHH--


    Download alignment FASTA file