Interaction between Cytochrome c iso-1 (6p42_D) and Cytochrome c peroxidase, mitochondrial (6p42_C)

PDB and SCOP data

PDB ID: 6p42 (all binary interactions in this PDB entry)

Title: Yeast cytochrome c peroxidase (W191Y:L232H) in complex with iso-1 cytochrome c

Release date: 2019-10-23

Resolution: 2.9 Å

  • Chain A: 6p42_D

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 103

  • Chain B: 6p42_C

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 581.07 Å2

Number of inter-residue contacts at the interface: 51

Number of H-bonds: 4

Number of salt bridges: 2

  • 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 6p42_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 5 K 10.5 11.6 %
    2 8 8 T 13.4 17.7 %
    3 9 9 L 23.0 82.3 %
    4 11 11 K 1.1 0.9 %
    5 12 12 T 53.9 68.9 %
    6 13 13 R 60.9 74.5 %
    7 16 16 Q 42.0 50.5 %
    8 17 17 C 3.0 75.9 %
    9 27 27 K 45.5 35.9 %
    10 28 28 V 24.4 33.2 %
    11 70 70 N 20.7 47.8 %
    12 72 72 K 30.5 32.7 %
    13 73 73 K 31.7 19.6 %
    14 81 81 A 52.8 73.6 %
    15 82 82 F 8.7 67.1 %
    16 83 83 G 34.9 48.9 %
    17 85 85 L 1.4 23.8 %
    18 86 86 K 81.5 57.5 %
    19 87 87 K 36.7 46.5 %
    20 90 90 D 4.3 35.0 %

  • Interface residues in 6p42_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 48.9 39.6 %
    2 32 32 E 32.5 32.4 %
    3 34 34 D 39.8 60.0 %
    4 35 35 E 18.5 14.7 %
    5 38 38 N 27.4 19.3 %
    6 39 39 Y 94.9 67.4 %
    7 120 120 Q 46.8 42.1 %
    8 192 192 G 1.3 39.6 %
    9 193 193 A 32.9 78.8 %
    10 194 194 A 17.7 88.9 %
    11 195 195 N 23.1 52.1 %
    12 196 196 N 25.9 47.2 %
    13 197 197 V 42.0 88.7 %
    14 199 199 T 14.2 35.2 %
    15 201 201 E 1.7 8.5 %
    16 205 205 N 1.4 5.4 %
    17 209 209 E 2.6 6.5 %
    18 227 227 S 35.8 54.8 %
    19 229 229 Y 25.8 90.7 %
    20 290 290 E 47.0 35.2 %
    21 294 294 L 0.9 0.8 %

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 5 5 K 35 35 E 0.2
2 5 5 K 39 39 Y 10.3
3 8 8 T 39 39 Y 13.4
4 9 9 L 39 39 Y 23.0
5 11 11 K 38 38 N 1.1
6 12 12 T 38 38 N 26.3
7 12 12 T 39 39 Y 19.2
8 12 12 T 195 195 N 8.4
9 13 13 R 34 34 D 15.5
10 13 13 R 39 39 Y 29.0
11 13 13 R 195 195 N <0.1
12 13 13 R 196 196 N 16.5
13 16 16 Q 192 192 G 1.3
14 16 16 Q 193 193 A 19.0 H-bond
15 16 16 Q 194 194 A 0.5
16 16 16 Q 195 195 N 14.7
17 16 16 Q 227 227 S 1.3
18 16 16 Q 229 229 Y 5.1
19 17 17 C 193 193 A 3.0
20 27 27 K 227 227 S 33.8
21 27 27 K 229 229 Y 11.8
22 28 28 V 193 193 A 10.8
23 28 28 V 205 205 N 1.4
24 28 28 V 209 209 E 2.6
25 28 28 V 227 227 S 0.7
26 28 28 V 229 229 Y 8.9
27 70 70 N 120 120 Q 4.5
28 70 70 N 290 290 E 16.2 H-bond
29 72 72 K 120 120 Q 25.7 H-bond
30 72 72 K 197 197 V 4.7
31 73 73 K 290 290 E 30.7
32 73 73 K 294 294 L 0.9
33 81 81 A 194 194 A 17.2
34 81 81 A 197 197 V 19.7
35 81 81 A 199 199 T 14.2
36 81 81 A 201 201 E 1.7
37 82 82 F 120 120 Q 1.7
38 82 82 F 196 196 N 0.4
39 82 82 F 197 197 V 6.6
40 83 83 G 120 120 Q 14.8
41 83 83 G 196 196 N 9.1
42 83 83 G 197 197 V 11.0
43 85 85 L 34 34 D 1.4
44 86 86 K 31 31 R 48.3
45 86 86 K 32 32 E 28.4 H-bond, Salt bridge
46 86 86 K 34 34 D 4.9
47 87 87 K 31 31 R 0.5
48 87 87 K 32 32 E 4.2
49 87 87 K 34 34 D 13.8
50 87 87 K 35 35 E 18.2 Salt bridge
51 90 90 D 34 34 D 4.3

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A6p42_D201HEM 638.625.3

  • 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: 6p42_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

    6p42_D: 1 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 60

    dssp: ----HHHHHHHHH---------------------HHH-----------------------


    Query: 67 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    6p42_D: 61 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 103

    dssp: --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: 6p42_C; Cytochrome c peroxidase, mitochondrial

    Alignment data:

    Expectation value = 0, Score = 606 bits (1562),

    Identities = 99% (290/294), Positive = 99% (291/294), Gaps = 0% (0/294).

    Interface alignment data:

    Interface residues in alignment: 100% (21/21).

    Identities = 100% (21/21), Positive = 100% (21/21), Gaps = 0% (0/21).

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    6p42_C: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

    dssp: -----EE--------HHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHH-----


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    6p42_C: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    6p42_C: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP+GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMM PTDYSLIQ

    6p42_C: 181 HLKNSGYEGPYGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMHPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    6p42_C: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file