Interaction between Cytochrome c iso-1 (6p43_B) and Cytochrome c peroxidase, mitochondrial (6p43_A)

PDB and SCOP data

PDB ID: 6p43 (all binary interactions in this PDB entry)

Title: Yeast cytochrome c peroxidase in complex with iso-1 cytochrome c (Y48K)

Release date: 2019-10-23

Resolution: 1.9 Å

  • Chain A: 6p43_B

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 108

  • Chain B: 6p43_A

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 502.28 Å2

Number of inter-residue contacts at the interface: 44

Number of H-bonds: 1

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 3 proteins.

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Create a structural model for this interaction

  • Interface residues in 6p43_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 10 K 11.8 15.8 %
    2 8 13 T 17.1 26.6 %
    3 9 14 L 21.3 98.5 %
    4 11 16 K 5.7 4.6 %
    5 12 17 T 47.9 72.0 %
    6 13 18 R 55.4 67.2 %
    7 16 21 Q 41.8 45.8 %
    8 17 22 C 6.0 100.0 %
    9 27 32 K 0.6 0.7 %
    10 28 33 V 25.8 29.2 %
    11 70 75 N 27.9 53.1 %
    12 72 77 K 44.6 33.4 %
    13 73 78 K 8.1 5.0 %
    14 81 86 A 46.8 77.0 %
    15 82 87 F 17.2 76.1 %
    16 83 88 G 34.6 60.4 %
    17 86 91 K 53.3 41.8 %
    18 87 92 K 19.0 16.5 %
    19 90 95 D 17.2 72.8 %

  • Interface residues in 6p43_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 50.2 33.9 %
    2 34 34 D 34.0 48.1 %
    3 35 35 E 8.0 6.8 %
    4 38 38 N 32.0 23.4 %
    5 39 39 Y 105.3 78.1 %
    6 120 120 Q 57.4 49.9 %
    7 192 192 G <0.1 0.5 %
    8 193 193 A 45.5 89.1 %
    9 194 194 A 17.6 77.9 %
    10 195 195 N 6.5 24.9 %
    11 196 196 N 25.7 48.3 %
    12 197 197 V 43.2 98.2 %
    13 198 198 F 2.1 57.2 %
    14 199 199 T 19.0 55.8 %
    15 201 201 E 0.5 2.2 %
    16 227 227 S 0.6 0.9 %
    17 229 229 Y 21.6 53.7 %
    18 290 290 E 29.5 21.1 %
    19 294 294 L 3.4 2.6 %

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 10 K 35 35 E 1.1
2 5 10 K 39 39 Y 10.6
3 8 13 T 39 39 Y 17.1
4 9 14 L 39 39 Y 21.3
5 11 16 K 38 38 N 5.7
6 12 17 T 38 38 N 26.3
7 12 17 T 39 39 Y 21.6
8 13 18 R 34 34 D 10.3
9 13 18 R 39 39 Y 29.5
10 13 18 R 196 196 N 15.5
11 16 21 Q 192 192 G <0.1
12 16 21 Q 193 193 A 28.2
13 16 21 Q 195 195 N 6.5
14 16 21 Q 229 229 Y 7.1
15 17 22 C 193 193 A 6.0
16 27 32 K 227 227 S 0.6
17 28 33 V 193 193 A 11.3
18 28 33 V 229 229 Y 14.5
19 70 75 N 120 120 Q 6.9
20 70 75 N 290 290 E 21.1
21 72 77 K 120 120 Q 28.4 H-bond
22 72 77 K 197 197 V 8.1
23 72 77 K 198 198 F 2.1
24 72 77 K 199 199 T 5.8
25 72 77 K 290 290 E 0.2
26 73 78 K 290 290 E 8.1
27 81 86 A 194 194 A 17.6
28 81 86 A 197 197 V 15.5
29 81 86 A 199 199 T 13.2
30 81 86 A 201 201 E 0.5
31 82 87 F 120 120 Q 8.6
32 82 87 F 196 196 N 1.4
33 82 87 F 197 197 V 7.2
34 83 88 G 120 120 Q 13.5
35 83 88 G 196 196 N 8.8
36 83 88 G 197 197 V 12.4
37 86 91 K 31 31 R 49.8
38 86 91 K 290 290 E <0.1
39 86 91 K 294 294 L 3.4
40 87 92 K 31 31 R 0.5
41 87 92 K 34 34 D 11.6
42 87 92 K 35 35 E 6.9
43 90 95 D 34 34 D 12.0
44 90 95 D 39 39 Y 5.2

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A6p43_B201HEM 614.928.8

  • 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: 6p43_B; Cytochrome c iso-1

    Alignment data:

    Expectation value = 2.71e-75, Score = 220 bits (560),

    Identities = 98% (106/108), Positive = 98% (106/108), Gaps = 0% (0/108).

    Interface alignment data:

    Interface residues in alignment: 100% (19/19).

    Identities = 100% (19/19), Positive = 100% (19/19), Gaps = 0% (0/19).

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYS TDANIKK

    6p43_B: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSKTDANIKK 60

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


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKA E

    6p43_B: 61 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKASE 108

    dssp: --E----HHHHH---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: 6p43_A; Cytochrome c peroxidase, mitochondrial

    Alignment data:

    Expectation value = 0, Score = 611 bits (1575),

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

    Interface alignment data:

    Interface residues in alignment: 100% (19/19).

    Identities = 100% (19/19), Positive = 100% (19/19), Gaps = 0% (0/19).

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    6p43_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    6p43_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    6p43_A: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    6p43_A: 181 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    6p43_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

    dssp: -HHHHHHHHHHHH-HHHHHHHHHHHHHHHHH--EE--------E-----HHH--


    Download alignment FASTA file