Interaction between Cytochrome c iso-1 (5cib_D) 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_D

    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: 471.00 Å2

Number of inter-residue contacts at the interface: 42

Number of H-bonds: 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 5cib_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 8 13 T 7.1 12.3 %
    2 9 14 L 30.6 79.2 %
    3 12 17 T 56.7 63.9 %
    4 13 18 R 36.1 75.2 %
    5 16 21 Q 37.7 43.1 %
    6 17 22 C 3.9 96.1 %
    7 28 33 V 29.0 29.0 %
    8 70 75 N 34.7 58.3 %
    9 71 76 P 1.6 16.6 %
    10 72 77 K 16.2 16.9 %
    11 81 86 A 42.1 60.2 %
    12 82 87 F 25.2 81.7 %
    13 83 88 G 36.3 47.8 %
    14 84 89 G 13.9 54.2 %
    15 85 90 L 4.5 23.6 %
    16 86 91 K 53.9 32.9 %
    17 87 92 K 31.5 26.8 %
    18 90 95 D 10.1 51.4 %

  • Interface residues in 5cib_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 41.7 39.8 %
    2 32 32 E 5.6 4.4 %
    3 34 34 D 27.0 41.1 %
    4 35 35 E 16.0 12.2 %
    5 38 38 N 34.1 24.7 %
    6 39 39 Y 97.7 67.8 %
    7 40 40 I <0.1 0.1 %
    8 120 120 Q 36.4 30.9 %
    9 193 193 A 40.5 90.6 %
    10 194 194 A 15.1 65.4 %
    11 195 195 N 3.1 13.1 %
    12 196 196 N 38.5 64.4 %
    13 197 197 V 37.1 91.9 %
    14 199 199 T 11.1 31.8 %
    15 201 201 E 3.8 13.6 %
    16 229 229 Y 23.1 57.5 %
    17 290 290 E 28.5 22.2 %
    18 294 294 L 11.7 10.4 %

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 8 13 T 39 39 Y 7.1
2 9 14 L 39 39 Y 30.6
3 12 17 T 38 38 N 34.1
4 12 17 T 39 39 Y 22.5
5 12 17 T 40 40 I <0.1
6 13 18 R 39 39 Y 24.5
7 13 18 R 196 196 N 11.6
8 16 21 Q 193 193 A 25.8
9 16 21 Q 195 195 N 3.1
10 16 21 Q 229 229 Y 8.7
11 17 22 C 193 193 A 3.9
12 28 33 V 193 193 A 10.7
13 28 33 V 201 201 E 3.8
14 28 33 V 229 229 Y 14.4
15 70 75 N 120 120 Q 7.9
16 70 75 N 290 290 E 26.8 H-bond
17 71 76 P 120 120 Q 1.6
18 72 77 K 120 120 Q 14.5
19 72 77 K 290 290 E 1.7
20 81 86 A 194 194 A 14.0
21 81 86 A 197 197 V 17.0
22 81 86 A 199 199 T 11.1
23 82 87 F 120 120 Q 7.4
24 82 87 F 194 194 A 1.1
25 82 87 F 196 196 N 2.2
26 82 87 F 197 197 V 14.4
27 83 88 G 34 34 D 1.0
28 83 88 G 120 120 Q 4.9
29 83 88 G 196 196 N 24.6
30 83 88 G 197 197 V 5.7
31 84 89 G 34 34 D 13.9
32 85 90 L 34 34 D 4.5
33 86 91 K 31 31 R 41.0
34 86 91 K 34 34 D 1.2
35 86 91 K 294 294 L 11.7
36 87 92 K 31 31 R 0.7
37 87 92 K 32 32 E 5.6
38 87 92 K 34 34 D 6.0
39 87 92 K 35 35 E 16.0
40 87 92 K 39 39 Y 3.1
41 90 95 D 34 34 D 0.3
42 90 95 D 39 39 Y 9.8

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A5cib_D201HEM 642.221.8

  • 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_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% (18/18).

    Identities = 100% (18/18), Positive = 100% (18/18), Gaps = 0% (0/18).

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    5cib_D: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

    dssp: ---------HHHHHHH-------E-----------E------------------------


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    5cib_D: 61 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 108

    dssp: ---------------HHHH-------------HHHHHHHHHH------


    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% (18/18).

    Identities = 100% (18/18), Positive = 100% (18/18), Gaps = 0% (0/18).

    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