Interaction between Cytochrome c iso-1 (5cid_B) and Cytochrome c peroxidase, mitochondrial (5cid_A)

PDB and SCOP data

PDB ID: 5cid (all binary interactions in this PDB entry)

Title: Complex of yeast cytochrome c peroxidase (W191G) bound to o-toluidine with iso-1 cytochrome c

Release date: 2016-08-03

Resolution: 2.8 Å

  • Chain A: 5cid_B

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 108

  • Chain B: 5cid_A

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 538.19 Å2

Number of inter-residue contacts at the interface: 41

Number of H-bonds: 2

Number of salt bridges: 1

  • Pairwise interaction

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  • Biological assembly

    Heteromer, 4 proteins.

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Create a structural model for this interaction

  • Interface residues in 5cid_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 10 K 22.9 26.0 %
    2 8 13 T 11.7 16.4 %
    3 9 14 L 19.9 93.6 %
    4 12 17 T 50.1 64.2 %
    5 13 18 R 61.0 72.9 %
    6 16 21 Q 40.9 41.7 %
    7 17 22 C 8.4 100.0 %
    8 28 33 V 24.1 28.0 %
    9 70 75 N 23.9 49.3 %
    10 72 77 K 26.4 20.6 %
    11 73 78 K 21.4 12.4 %
    12 81 86 A 48.7 73.2 %
    13 82 87 F 23.7 82.3 %
    14 83 88 G 29.3 51.1 %
    15 86 91 K 54.1 47.1 %
    16 87 92 K 56.7 44.4 %
    17 90 95 D 14.9 55.8 %

  • Interface residues in 5cid_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 56.1 43.5 %
    2 32 32 E 26.9 21.8 %
    3 34 34 D 44.7 67.9 %
    4 35 35 E 10.9 9.3 %
    5 38 38 N 29.6 21.3 %
    6 39 39 Y 99.2 78.9 %
    7 120 120 Q 49.0 45.2 %
    8 193 193 A 51.1 93.1 %
    9 194 194 A 14.9 73.7 %
    10 195 195 N 6.5 29.1 %
    11 196 196 N 26.9 48.3 %
    12 197 197 V 38.8 88.3 %
    13 199 199 T 12.6 38.0 %
    14 201 201 E 0.4 1.5 %
    15 229 229 Y 15.5 44.2 %
    16 290 290 E 48.4 38.6 %
    17 294 294 L 6.7 5.4 %

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 10.0
2 5 10 K 39 39 Y 12.9
3 8 13 T 39 39 Y 11.7
4 9 14 L 39 39 Y 19.9
5 12 17 T 38 38 N 29.6
6 12 17 T 39 39 Y 20.5
7 13 18 R 34 34 D 15.3
8 13 18 R 39 39 Y 29.9
9 13 18 R 196 196 N 15.8
10 16 21 Q 193 193 A 31.3
11 16 21 Q 195 195 N 6.5
12 16 21 Q 229 229 Y 3.2
13 17 22 C 193 193 A 8.4
14 28 33 V 193 193 A 11.5
15 28 33 V 201 201 E 0.4
16 28 33 V 229 229 Y 12.3
17 70 75 N 290 290 E 23.5
18 70 75 N 294 294 L 0.4
19 72 77 K 120 120 Q 24.7
20 72 77 K 290 290 E 1.7
21 73 78 K 290 290 E 21.4
22 81 86 A 120 120 Q 0.6
23 81 86 A 194 194 A 14.9
24 81 86 A 196 196 N 1.2
25 81 86 A 197 197 V 19.4
26 81 86 A 199 199 T 12.6
27 82 87 F 120 120 Q 11.8
28 82 87 F 196 196 N 3.9
29 82 87 F 197 197 V 8.0
30 83 88 G 120 120 Q 11.9
31 83 88 G 196 196 N 6.0
32 83 88 G 197 197 V 11.4
33 86 91 K 31 31 R 45.9
34 86 91 K 290 290 E 1.8
35 86 91 K 294 294 L 6.3
36 87 92 K 31 31 R 10.2
37 87 92 K 32 32 E 26.9 H-bond
38 87 92 K 34 34 D 18.7 H-bond, Salt bridge
39 87 92 K 35 35 E 0.9
40 90 95 D 34 34 D 10.7
41 90 95 D 39 39 Y 4.2

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A5cid_B201HEM 629.724.2

  • 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: 5cid_B; Cytochrome c iso-1

    Alignment data:

    Expectation value = 1.54e-77, Score = 226 bits (575),

    Identities = 100% (108/108), Positive = 100% (108/108), Gaps = 0% (0/108).

    Interface alignment data:

    Interface residues in alignment: 100% (17/17).

    Identities = 100% (17/17), Positive = 100% (17/17), Gaps = 0% (0/17).

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    5cid_B: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

    dssp: -------HHHHHHHHHHH-------------------------E----------HHHHH-


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    5cid_B: 61 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 108

    dssp: --E--HHHHHHH---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: 5cid_A; Cytochrome c peroxidase, mitochondrial

    Alignment data:

    Expectation value = 0, Score = 607 bits (1564),

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

    Interface alignment data:

    Interface residues in alignment: 100% (17/17).

    Identities = 100% (17/17), Positive = 100% (17/17), Gaps = 0% (0/17).

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    5cid_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    5cid_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    5cid_A: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    5cid_A: 181 HLKNSGYEGPGGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

    dssp: --------E-----------HHHHHHHH--EEEEE-----EEEEE----EE-HHHHHHHH


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    5cid_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file