Interaction between Cytochrome c iso-1 (5cih_D) and Cytochrome c peroxidase, mitochondrial (5cih_C)

PDB and SCOP data

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

Title: Complex of yeast cytochrome c peroxidase (W191Y) with iso-1 cytochrome c

Release date: 2016-08-03

Resolution: 2.6 Å

  • Chain A: 5cih_D

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 103

  • Chain B: 5cih_C

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 580.18 Å2

Number of inter-residue contacts at the interface: 54

Number of H-bonds: 1

Number of salt bridges: 3

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 2 proteins.

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Create a structural model for this interaction

  • Interface residues in 5cih_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 5 K 21.1 23.1 %
    2 8 8 T 12.9 19.1 %
    3 9 9 L 20.7 85.2 %
    4 12 12 T 43.8 50.4 %
    5 13 13 R 50.4 65.5 %
    6 16 16 Q 41.5 47.4 %
    7 17 17 C 6.4 100.0 %
    8 27 27 K 34.9 34.8 %
    9 28 28 V 27.3 42.8 %
    10 70 70 N 18.5 32.8 %
    11 71 71 P 4.1 29.1 %
    12 72 72 K 1.8 1.4 %
    13 73 73 K 31.1 20.7 %
    14 79 79 K 1.1 1.0 %
    15 81 81 A 50.3 79.0 %
    16 82 82 F 28.1 87.3 %
    17 83 83 G 32.5 48.2 %
    18 86 86 K 80.6 52.7 %
    19 87 87 K 56.8 47.1 %
    20 90 90 D 16.4 57.5 %

  • Interface residues in 5cih_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 28 28 L 7.5 9.1 %
    2 31 31 R 53.5 42.5 %
    3 32 32 E 41.8 40.1 %
    4 33 33 D 0.9 1.4 %
    5 34 34 D 45.5 61.0 %
    6 35 35 E 16.1 12.3 %
    7 38 38 N 26.3 19.3 %
    8 39 39 Y 94.3 67.7 %
    9 120 120 Q 35.9 29.6 %
    10 193 193 A 35.0 93.5 %
    11 194 194 A 18.5 87.7 %
    12 195 195 N 4.3 17.1 %
    13 196 196 N 36.4 58.4 %
    14 197 197 V 36.7 93.1 %
    15 199 199 T 16.0 40.0 %
    16 201 201 E 5.9 19.4 %
    17 226 226 K 26.0 18.6 %
    18 227 227 S 15.3 21.2 %
    19 229 229 Y 22.6 71.7 %
    20 290 290 E 41.7 29.6 %

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 5 K 35 35 E 7.3
2 5 5 K 39 39 Y 13.7
3 8 8 T 39 39 Y 12.9
4 9 9 L 39 39 Y 20.7
5 12 12 T 38 38 N 26.3
6 12 12 T 39 39 Y 17.1
7 12 12 T 195 195 N 0.3
8 13 13 R 34 34 D 7.7
9 13 13 R 38 38 N <0.1
10 13 13 R 39 39 Y 26.4
11 13 13 R 196 196 N 16.3
12 16 16 Q 193 193 A 20.5
13 16 16 Q 194 194 A 1.3
14 16 16 Q 195 195 N 4.0
15 16 16 Q 227 227 S 4.3
16 16 16 Q 229 229 Y 11.4
17 17 17 C 193 193 A 6.4
18 17 17 C 229 229 Y <0.1
19 27 27 K 226 226 K 22.9
20 27 27 K 227 227 S 11.0
21 27 27 K 229 229 Y 1.0
22 28 28 V 193 193 A 8.0
23 28 28 V 201 201 E 5.9
24 28 28 V 226 226 K 3.2
25 28 28 V 229 229 Y 10.2
26 70 70 N 120 120 Q 8.0
27 70 70 N 290 290 E 10.5
28 71 71 P 120 120 Q 4.1
29 72 72 K 120 120 Q 1.8
30 73 73 K 290 290 E 31.1 Salt bridge
31 79 79 K 199 199 T 1.1
32 81 81 A 120 120 Q 0.9
33 81 81 A 194 194 A 17.2
34 81 81 A 196 196 N 0.1
35 81 81 A 197 197 V 17.1
36 81 81 A 199 199 T 14.9
37 82 82 F 120 120 Q 11.4
38 82 82 F 196 196 N 5.8
39 82 82 F 197 197 V 10.9
40 83 83 G 120 120 Q 9.7
41 83 83 G 196 196 N 14.1
42 83 83 G 197 197 V 8.6
43 86 86 K 28 28 L 7.5
44 86 86 K 31 31 R 49.8
45 86 86 K 32 32 E 19.6 Salt bridge
46 86 86 K 34 34 D 3.6
47 87 87 K 31 31 R 3.6
48 87 87 K 32 32 E 22.2 H-bond
49 87 87 K 33 33 D 0.9
50 87 87 K 34 34 D 25.1 Salt bridge
51 87 87 K 35 35 E 5.0
52 90 90 D 34 34 D 9.1
53 90 90 D 35 35 E 3.8
54 90 90 D 39 39 Y 3.5

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A5cih_D201HEM 632.127.5

  • 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: 5cih_D; Cytochrome c iso-1

    Alignment data:

    Expectation value = 6.80e-74, Score = 216 bits (550),

    Identities = 100% (103/103), Positive = 100% (103/103), Gaps = 0% (0/103).

    Interface alignment data:

    Interface residues in alignment: 100% (20/20).

    Identities = 100% (20/20), Positive = 100% (20/20), Gaps = 0% (0/20).

    Query: 7 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 66

    GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD

    5cih_D: 1 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 60

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


    Query: 67 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    5cih_D: 61 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 103

    dssp: HHHHHHHH-------------------HHHHHHHHHHHHH---


    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: 5cih_C; Cytochrome c peroxidase, mitochondrial

    Alignment data:

    Expectation value = 0, Score = 609 bits (1568),

    Identities = 99% (291/294), Positive = 99% (292/294), Gaps = 0% (0/294).

    Interface alignment data:

    Interface residues in alignment: 100% (20/20).

    Identities = 100% (20/20), Positive = 100% (20/20), Gaps = 0% (0/20).

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    5cih_C: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    5cih_C: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    5cih_C: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

    dssp: -----E--------HHH-------------HHHHHHHHHH----HHHHHHHHHHHH--EE


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP+GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    5cih_C: 181 HLKNSGYEGPYGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    5cih_C: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file