Interaction between Cytochrome c iso-1 (6p41_D) and Cytochrome c peroxidase, mitochondrial (6p41_C)

PDB and SCOP data

PDB ID: 6p41 (all binary interactions in this PDB entry)

Title: Yeast cytochrome c peroxidase (W191Y:L232E) in complex with iso-1 cytochrome c

Release date: 2019-10-23

Resolution: 2.9 Å

  • Chain A: 6p41_D

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 103

  • Chain B: 6p41_C

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 525.82 Å2

Number of inter-residue contacts at the interface: 45

Number of H-bonds: 1

Number of salt bridges: 1

  • 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 6p41_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 5 K 22.7 20.8 %
    2 8 8 T 11.5 14.6 %
    3 9 9 L 24.8 99.8 %
    4 12 12 T 57.8 62.4 %
    5 13 13 R 56.7 72.6 %
    6 16 16 Q 47.2 45.6 %
    7 17 17 C 4.4 99.7 %
    8 27 27 K 2.1 1.8 %
    9 28 28 V 26.4 33.2 %
    10 70 70 N 19.1 33.6 %
    11 72 72 K 36.0 26.7 %
    12 73 73 K 11.3 7.3 %
    13 81 81 A 47.4 67.6 %
    14 82 82 F 15.0 51.5 %
    15 83 83 G 31.3 58.8 %
    16 85 85 L 9.3 75.7 %
    17 86 86 K 48.6 37.4 %
    18 87 87 K 48.4 35.4 %
    19 90 90 D 5.9 41.4 %

  • Interface residues in 6p41_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 39.8 36.3 %
    2 32 32 E 20.4 18.3 %
    3 34 34 D 42.0 75.3 %
    4 35 35 E 17.6 12.9 %
    5 38 38 N 31.4 22.3 %
    6 39 39 Y 100.0 77.5 %
    7 40 40 I 0.7 5.3 %
    8 120 120 Q 51.4 46.5 %
    9 193 193 A 42.1 94.5 %
    10 194 194 A 13.9 81.9 %
    11 195 195 N 21.2 51.9 %
    12 196 196 N 24.3 47.3 %
    13 197 197 V 39.8 95.3 %
    14 199 199 T 17.8 45.4 %
    15 201 201 E 0.3 1.4 %
    16 227 227 S 4.6 6.5 %
    17 229 229 Y 17.7 64.3 %
    18 290 290 E 32.3 23.1 %
    19 294 294 L 8.6 7.0 %

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 5 K 35 35 E 10.6
2 5 5 K 39 39 Y 12.1
3 8 8 T 39 39 Y 11.5
4 9 9 L 39 39 Y 24.8
5 12 12 T 38 38 N 31.4
6 12 12 T 39 39 Y 19.8
7 12 12 T 40 40 I 0.7
8 12 12 T 195 195 N 5.8
9 13 13 R 34 34 D 11.8
10 13 13 R 39 39 Y 30.4
11 13 13 R 196 196 N 14.5
12 16 16 Q 193 193 A 30.1 H-bond
13 16 16 Q 195 195 N 15.4
14 16 16 Q 229 229 Y 1.7
15 17 17 C 193 193 A 4.4
16 27 27 K 227 227 S 2.1
17 28 28 V 193 193 A 7.6
18 28 28 V 201 201 E 0.3
19 28 28 V 227 227 S 2.6
20 28 28 V 229 229 Y 16.1
21 70 70 N 120 120 Q 2.9
22 70 70 N 290 290 E 16.2
23 72 72 K 120 120 Q 34.8
24 72 72 K 199 199 T 1.2
25 73 73 K 290 290 E 11.3
26 81 81 A 194 194 A 13.9
27 81 81 A 197 197 V 16.9
28 81 81 A 199 199 T 16.6
29 82 82 F 120 120 Q 3.5
30 82 82 F 196 196 N 2.8
31 82 82 F 197 197 V 8.7
32 83 83 G 120 120 Q 10.2
33 83 83 G 196 196 N 7.0
34 83 83 G 197 197 V 14.1
35 85 85 L 34 34 D 8.5
36 85 85 L 39 39 Y 0.8
37 86 86 K 31 31 R 35.2
38 86 86 K 290 290 E 4.8
39 86 86 K 294 294 L 8.6
40 87 87 K 31 31 R 4.6
41 87 87 K 32 32 E 20.4
42 87 87 K 34 34 D 16.4 Salt bridge
43 87 87 K 35 35 E 7.0
44 90 90 D 34 34 D 5.3
45 90 90 D 39 39 Y 0.6

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A6p41_D201HEM 654.723.1

  • 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: 6p41_D; Cytochrome c iso-1

    Alignment data:

    Expectation value = 9.90e-73, Score = 214 bits (543),

    Identities = 99% (102/103), Positive = 99% (102/103), Gaps = 0% (0/103).

    Interface alignment data:

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

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

    Query: 7 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 66

    GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD

    6p41_D: 1 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 60

    dssp: ----HHHHHHHHH-------------------------------------HHHHH-----


    Query: 67 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKA E

    6p41_D: 61 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKASE 103

    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: 6p41_C; Cytochrome c peroxidase, mitochondrial

    Alignment data:

    Expectation value = 0, Score = 606 bits (1561),

    Identities = 99% (290/294), Positive = 99% (291/294), 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

    6p41_C: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    6p41_C: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

    dssp: --E------HHH-HHHH--HHH---HHHHHHHHHHHHH-----HHHHHHHHHHHHHH---


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    6p41_C: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP+GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMM PTDYSLIQ

    6p41_C: 181 HLKNSGYEGPYGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMEPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    6p41_C: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

    dssp: -HHHHHHHHHHHH-HHHHHHHHHHHHHHH-----E--------E----------


    Download alignment FASTA file