Interaction between Cytochrome c iso-1 (6p42_B) and Cytochrome c peroxidase, mitochondrial (6p42_A)

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_B

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 103

  • Chain B: 6p42_A

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 551.67 Å2

Number of inter-residue contacts at the interface: 47

Number of H-bonds: 2

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_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 5 K 16.9 18.0 %
    2 8 8 T 16.0 20.5 %
    3 9 9 L 19.9 98.5 %
    4 12 12 T 58.2 74.6 %
    5 13 13 R 60.6 71.5 %
    6 16 16 Q 43.2 46.0 %
    7 17 17 C 4.6 96.5 %
    8 27 27 K 6.9 5.6 %
    9 28 28 V 27.1 32.5 %
    10 70 70 N 21.6 58.7 %
    11 71 71 P 4.2 68.1 %
    12 72 72 K 55.9 42.8 %
    13 73 73 K 3.5 2.6 %
    14 81 81 A 50.5 69.5 %
    15 82 82 F 23.3 81.6 %
    16 83 83 G 33.3 59.6 %
    17 86 86 K 56.0 46.1 %
    18 87 87 K 43.1 35.3 %
    19 90 90 D 6.8 61.2 %

  • Interface residues in 6p42_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 57.0 50.4 %
    2 32 32 E 5.4 4.7 %
    3 34 34 D 42.9 66.0 %
    4 38 38 N 27.7 21.1 %
    5 39 39 Y 108.9 79.2 %
    6 40 40 I <0.1 0.1 %
    7 120 120 Q 63.7 52.4 %
    8 192 192 G 1.6 40.8 %
    9 193 193 A 41.5 89.5 %
    10 194 194 A 16.0 82.3 %
    11 195 195 N 23.2 53.6 %
    12 196 196 N 27.9 55.5 %
    13 197 197 V 39.0 92.6 %
    14 199 199 T 16.0 41.9 %
    15 209 209 E 1.5 3.0 %
    16 227 227 S 6.8 9.7 %
    17 229 229 Y 15.3 46.3 %
    18 290 290 E 47.3 38.3 %
    19 294 294 L 9.9 8.1 %

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 39 39 Y 16.9
2 8 8 T 39 39 Y 16.0
3 9 9 L 39 39 Y 19.9
4 12 12 T 38 38 N 27.7
5 12 12 T 39 39 Y 22.5
6 12 12 T 40 40 I <0.1
7 12 12 T 195 195 N 8.1
8 13 13 R 34 34 D 11.4
9 13 13 R 39 39 Y 29.9
10 13 13 R 196 196 N 19.4
11 16 16 Q 192 192 G 1.6
12 16 16 Q 193 193 A 24.9
13 16 16 Q 194 194 A <0.1
14 16 16 Q 195 195 N 15.2
15 16 16 Q 229 229 Y 1.5
16 17 17 C 193 193 A 4.6
17 27 27 K 209 209 E 0.1
18 27 27 K 227 227 S 6.8
19 28 28 V 193 193 A 12.0
20 28 28 V 209 209 E 1.3
21 28 28 V 229 229 Y 13.8
22 70 70 N 120 120 Q 0.6
23 70 70 N 290 290 E 18.8 H-bond
24 70 70 N 294 294 L 2.3
25 71 71 P 120 120 Q 4.2
26 72 72 K 120 120 Q 31.5
27 72 72 K 290 290 E 24.4 H-bond, Salt bridge
28 73 73 K 290 290 E 3.5
29 81 81 A 120 120 Q 1.6
30 81 81 A 194 194 A 16.0
31 81 81 A 197 197 V 16.9
32 81 81 A 199 199 T 16.0
33 82 82 F 120 120 Q 11.3
34 82 82 F 196 196 N 1.7
35 82 82 F 197 197 V 10.3
36 83 83 G 120 120 Q 14.6
37 83 83 G 196 196 N 6.9
38 83 83 G 197 197 V 11.8
39 86 86 K 31 31 R 47.8
40 86 86 K 290 290 E 0.6
41 86 86 K 294 294 L 7.7
42 87 87 K 31 31 R 9.2
43 87 87 K 32 32 E 5.4
44 87 87 K 34 34 D 25.8 Salt bridge
45 87 87 K 39 39 Y 2.7
46 90 90 D 34 34 D 5.8
47 90 90 D 39 39 Y 1.0

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A6p42_B201HEM 640.228.1

  • 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: 6p42_B; 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% (19/19).

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

    Query: 7 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 66

    GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD

    6p42_B: 1 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 60

    dssp: ----HHHHHHHHH------------------------------------HHHH-------


    Query: 67 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    6p42_B: 61 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 103

    dssp: HHHHHHHHH-HHHH--------------HHHHHHHHHHHH---


    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_A; 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% (19/19).

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

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    6p42_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

    dssp: ------E--------HHHHHHHHHHHHHHHHH---HHHH---HHHHHHHHHHHHH--E--


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    6p42_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    6p42_A: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP+GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMM PTDYSLIQ

    6p42_A: 181 HLKNSGYEGPYGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMHPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    6p42_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file