Interaction between Cytochrome c iso-1 (5cic_B) and Cytochrome c peroxidase, mitochondrial (5cic_C)

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_B

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 108

  • Chain B: 5cic_C

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 232.90 Å2

Number of inter-residue contacts at the interface: 20

Number of H-bonds: 2

Number of salt bridges: 1

  • Pairwise interaction

    Download PDB coordinates

    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 4 proteins.

    Download PDB coordinates


Create a structural model for this interaction

  • Interface residues in 5cic_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 -5 1 T 11.5 8.2 %
    2 -4 2 E 41.1 28.8 %
    3 -2 4 K 21.0 13.3 %
    4 62 67 N 9.8 17.3 %
    5 66 71 E 41.2 44.4 %
    6 73 78 K 42.5 28.7 %
    7 86 91 K 1.5 1.1 %
    8 87 92 K 8.5 6.2 %
    9 88 93 E 49.1 48.8 %
    10 91 96 R 6.7 20.2 %

  • Interface residues in 5cic_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 29 29 K 25.7 48.9 %
    2 32 32 E 10.9 10.0 %
    3 33 33 D 22.9 45.4 %
    4 42 42 Y 14.5 44.3 %
    5 90 90 K 31.0 22.9 %
    6 93 93 E 25.9 40.6 %
    7 94 94 P 6.2 8.7 %
    8 97 97 K 56.4 39.2 %
    9 98 98 E 35.0 33.4 %
    10 99 99 F 2.3 10.9 %
    11 100 100 P 2.0 2.0 %

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 90 90 K 11.5
2 -4 2 E 90 90 K 13.0
3 -4 2 E 93 93 E 25.9
4 -4 2 E 97 97 K 2.2
5 -2 4 K 42 42 Y 14.5
6 -2 4 K 90 90 K 6.5
7 62 67 N 97 97 K 9.8
8 66 71 E 97 97 K 40.9
9 66 71 E 98 98 E 0.3
10 73 78 K 97 97 K 3.4
11 73 78 K 98 98 E 34.7 H-bond
12 73 78 K 99 99 F 2.3
13 73 78 K 100 100 P 2.0
14 86 91 K 32 32 E 1.5
15 87 92 K 32 32 E 8.5
16 88 93 E 29 29 K 25.2 H-bond, Salt bridge
17 88 93 E 32 32 E 1.0
18 88 93 E 33 33 D 22.9
19 91 96 R 29 29 K 0.5
20 91 96 R 94 94 P 6.2

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: 5cic_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% (10/10).

    Identities = 100% (10/10), Positive = 100% (10/10), Gaps = 0% (0/10).

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    5cic_B: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

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


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    5cic_B: 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_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

    5cic_C: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    5cic_C: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    5cic_C: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    5cic_C: 181 HLKNSGYEGPGGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    5cic_C: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file