Interaction between Cytochrome c iso-1 (5cig_D) and Cytochrome c peroxidase, mitochondrial (5cig_C)

PDB and SCOP data

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

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

Release date: 2016-08-03

Resolution: 2.1 Å

  • Chain A: 5cig_D

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 108

  • Chain B: 5cig_C

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 506.42 Å2

Number of inter-residue contacts at the interface: 39

Number of H-bonds: 2

Number of salt bridges: 1

  • Pairwise interaction

    Download PDB coordinates

    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 2 proteins.

    Download PDB coordinates


Create a structural model for this interaction

  • Interface residues in 5cig_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 10 K 17.4 18.2 %
    2 8 13 T 9.0 12.5 %
    3 9 14 L 21.2 95.8 %
    4 12 17 T 49.1 58.0 %
    5 13 18 R 62.3 73.6 %
    6 16 21 Q 36.6 39.3 %
    7 17 22 C 6.4 100.0 %
    8 28 33 V 23.4 27.6 %
    9 70 75 N 28.3 62.3 %
    10 72 77 K 20.5 19.2 %
    11 73 78 K 1.8 1.1 %
    12 81 86 A 53.3 72.8 %
    13 82 87 F 20.6 74.1 %
    14 83 88 G 33.9 61.0 %
    15 86 91 K 51.5 42.7 %
    16 87 92 K 54.6 43.0 %
    17 90 95 D 16.5 56.9 %

  • Interface residues in 5cig_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 57.0 44.9 %
    2 32 32 E 24.6 21.2 %
    3 34 34 D 49.6 69.9 %
    4 35 35 E 7.2 6.1 %
    5 38 38 N 24.1 17.6 %
    6 39 39 Y 103.4 77.3 %
    7 120 120 Q 47.8 39.9 %
    8 193 193 A 46.3 91.1 %
    9 194 194 A 12.8 63.3 %
    10 195 195 N 2.4 13.5 %
    11 196 196 N 28.4 46.2 %
    12 197 197 V 34.4 90.4 %
    13 199 199 T 14.4 35.1 %
    14 201 201 E 3.1 11.3 %
    15 229 229 Y 14.6 36.6 %
    16 290 290 E 36.1 25.3 %

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 10 K 35 35 E 7.2
2 5 10 K 39 39 Y 10.1
3 8 13 T 39 39 Y 9.0
4 9 14 L 39 39 Y 21.2
5 12 17 T 38 38 N 24.1
6 12 17 T 39 39 Y 25.0
7 13 18 R 34 34 D 17.1
8 13 18 R 39 39 Y 33.7
9 13 18 R 196 196 N 11.4
10 16 21 Q 193 193 A 27.7
11 16 21 Q 195 195 N 2.4
12 16 21 Q 229 229 Y 6.5
13 17 22 C 193 193 A 6.4
14 28 33 V 193 193 A 12.2
15 28 33 V 201 201 E 3.1
16 28 33 V 229 229 Y 8.2
17 70 75 N 120 120 Q 4.1
18 70 75 N 290 290 E 24.3 H-bond
19 72 77 K 120 120 Q 14.6
20 72 77 K 290 290 E 5.9
21 73 78 K 290 290 E 1.8
22 81 86 A 120 120 Q 3.6
23 81 86 A 194 194 A 12.8
24 81 86 A 196 196 N 0.1
25 81 86 A 197 197 V 22.3
26 81 86 A 199 199 T 14.4
27 82 87 F 120 120 Q 11.7
28 82 87 F 196 196 N 3.2
29 82 87 F 197 197 V 5.8
30 83 88 G 120 120 Q 13.9
31 83 88 G 196 196 N 13.7
32 83 88 G 197 197 V 6.4
33 86 91 K 31 31 R 47.4
34 86 91 K 290 290 E 4.1
35 87 92 K 31 31 R 9.6
36 87 92 K 32 32 E 24.6 H-bond
37 87 92 K 34 34 D 20.4 Salt bridge
38 90 95 D 34 34 D 12.2
39 90 95 D 39 39 Y 4.4

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A5cig_D201HEM 630.125.9

  • 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: 5cig_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% (17/17).

    Identities = 100% (17/17), Positive = 100% (17/17), Gaps = 0% (0/17).

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    5cig_D: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

    dssp: -------HHHHHHHHHHH------------------------------------HHHH--


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    5cig_D: 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: 5cig_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% (16/16).

    Identities = 100% (16/16), Positive = 100% (16/16), Gaps = 0% (0/16).

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    5cig_C: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    5cig_C: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    5cig_C: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

    dssp: -----E--------HHH-------------HHHHHHHHHHH---HHHHHHHHHHHH--EE


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    5cig_C: 181 HLKNSGYEGPGGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    5cig_C: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file