Interaction between Cytochrome c iso-1 (6p41_B) and Cytochrome c peroxidase, mitochondrial (6p41_A)

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_B

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 103

  • Chain B: 6p41_A

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 536.38 Å2

Number of inter-residue contacts at the interface: 43

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_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 8 8 T 10.1 13.1 %
    2 9 9 L 26.7 76.5 %
    3 12 12 T 57.8 61.3 %
    4 13 13 R 73.3 76.7 %
    5 16 16 Q 38.6 41.2 %
    6 17 17 C 6.2 100.0 %
    7 28 28 V 26.5 28.4 %
    8 70 70 N 22.8 44.4 %
    9 71 71 P 4.1 76.7 %
    10 72 72 K 12.8 10.0 %
    11 73 73 K 19.0 11.5 %
    12 80 80 M 0.2 2.6 %
    13 81 81 A 52.4 71.6 %
    14 82 82 F 28.9 94.5 %
    15 83 83 G 31.9 54.1 %
    16 86 86 K 54.0 42.3 %
    17 87 87 K 56.0 43.8 %
    18 90 90 D 14.9 34.6 %

  • Interface residues in 6p41_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 56.2 53.4 %
    2 32 32 E 22.5 19.2 %
    3 34 34 D 49.2 71.8 %
    4 35 35 E 8.7 7.4 %
    5 38 38 N 30.5 22.3 %
    6 39 39 Y 94.1 64.5 %
    7 40 40 I 4.1 18.4 %
    8 41 41 G 1.5 15.5 %
    9 120 120 Q 47.3 36.5 %
    10 193 193 A 46.0 92.3 %
    11 194 194 A 17.8 83.8 %
    12 195 195 N 8.2 24.0 %
    13 196 196 N 40.0 67.4 %
    14 197 197 V 33.4 94.6 %
    15 199 199 T 15.9 43.6 %
    16 209 209 E 1.0 1.7 %
    17 229 229 Y 19.3 56.6 %
    18 290 290 E 37.7 29.4 %
    19 294 294 L 3.0 2.8 %

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 8 T 39 39 Y 10.1
2 9 9 L 39 39 Y 26.7
3 12 12 T 38 38 N 30.5
4 12 12 T 39 39 Y 24.0
5 12 12 T 195 195 N 3.2
6 13 13 R 34 34 D 19.2
7 13 13 R 39 39 Y 28.7
8 13 13 R 40 40 I 4.1
9 13 13 R 41 41 G 1.5
10 13 13 R 196 196 N 19.9
11 16 16 Q 193 193 A 30.0
12 16 16 Q 195 195 N 5.0
13 16 16 Q 229 229 Y 3.6
14 17 17 C 193 193 A 6.2
15 28 28 V 193 193 A 9.8
16 28 28 V 209 209 E 1.0
17 28 28 V 229 229 Y 15.7
18 70 70 N 120 120 Q 4.1
19 70 70 N 290 290 E 18.7
20 71 71 P 120 120 Q 4.1
21 72 72 K 120 120 Q 12.8
22 73 73 K 290 290 E 19.0
23 80 80 M 120 120 Q 0.2
24 81 81 A 120 120 Q 3.3
25 81 81 A 194 194 A 17.8
26 81 81 A 196 196 N 3.0
27 81 81 A 197 197 V 12.4
28 81 81 A 199 199 T 15.9
29 82 82 F 120 120 Q 12.6
30 82 82 F 196 196 N 8.3
31 82 82 F 197 197 V 8.0
32 83 83 G 120 120 Q 10.1
33 83 83 G 196 196 N 8.8
34 83 83 G 197 197 V 13.0
35 86 86 K 31 31 R 47.8
36 86 86 K 34 34 D 3.3
37 86 86 K 294 294 L 3.0
38 87 87 K 31 31 R 8.4
39 87 87 K 32 32 E 22.5 H-bond
40 87 87 K 34 34 D 16.4 Salt bridge
41 87 87 K 35 35 E 8.7
42 90 90 D 34 34 D 10.3
43 90 90 D 39 39 Y 4.5

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A6p41_B201HEM 635.022.3

  • 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_B; 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% (18/18).

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

    Query: 7 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 66

    GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD

    6p41_B: 1 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 60

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


    Query: 67 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKA E

    6p41_B: 61 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKASE 103

    dssp: HHHHHHHH--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_A; 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_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    6p41_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    6p41_A: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP+GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMM PTDYSLIQ

    6p41_A: 181 HLKNSGYEGPYGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMEPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    6p41_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

    dssp: -HHHHHHHHHHHH-HHHHHHHHHHHHHHHH---EE--------E----------


    Download alignment FASTA file