Interaction between Cytochrome c iso-1 (5cid_D) and Cytochrome c peroxidase, mitochondrial (5cid_C)

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_D

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 108

  • Chain B: 5cid_C

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 531.93 Å2

Number of inter-residue contacts at the interface: 40

Number of H-bonds: 4

Number of salt bridges: 2

  • Pairwise interaction

    Download PDB coordinates

    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 4 proteins.

    Download PDB coordinates


Create a structural model for this interaction

  • Interface residues in 5cid_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 10 K 11.7 14.2 %
    2 8 13 T 15.2 24.6 %
    3 9 14 L 19.4 94.9 %
    4 12 17 T 51.6 57.8 %
    5 13 18 R 63.3 76.6 %
    6 16 21 Q 43.0 36.9 %
    7 17 22 C 6.6 60.4 %
    8 28 33 V 13.8 19.3 %
    9 70 75 N 21.5 68.6 %
    10 72 77 K 36.6 28.2 %
    11 73 78 K 19.2 12.2 %
    12 81 86 A 50.0 68.1 %
    13 82 87 F 26.0 80.3 %
    14 83 88 G 34.9 63.9 %
    15 86 91 K 52.4 43.2 %
    16 87 92 K 54.1 43.1 %
    17 90 95 D 12.5 59.2 %

  • Interface residues in 5cid_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 49.5 39.8 %
    2 32 32 E 25.9 22.4 %
    3 34 34 D 48.1 65.5 %
    4 38 38 N 25.5 18.8 %
    5 39 39 Y 103.5 71.8 %
    6 40 40 I 0.6 3.4 %
    7 120 120 Q 48.3 41.4 %
    8 192 192 G 0.1 4.7 %
    9 193 193 A 48.2 90.5 %
    10 194 194 A 17.2 75.5 %
    11 195 195 N 1.3 6.7 %
    12 196 196 N 27.7 50.4 %
    13 197 197 V 38.1 90.0 %
    14 199 199 T 15.6 42.6 %
    15 229 229 Y 13.9 34.7 %
    16 290 290 E 68.5 52.1 %

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 10 K 39 39 Y 11.7
2 8 13 T 39 39 Y 15.2
3 9 14 L 34 34 D <0.1
4 9 14 L 39 39 Y 19.4
5 12 17 T 38 38 N 25.5
6 12 17 T 39 39 Y 25.5
7 12 17 T 40 40 I 0.6
8 13 18 R 34 34 D 18.4
9 13 18 R 39 39 Y 29.8
10 13 18 R 196 196 N 15.0
11 16 21 Q 192 192 G 0.1
12 16 21 Q 193 193 A 30.3
13 16 21 Q 195 195 N 1.3
14 16 21 Q 229 229 Y 11.3
15 17 22 C 193 193 A 6.6
16 28 33 V 193 193 A 11.2
17 28 33 V 229 229 Y 2.6
18 70 75 N 120 120 Q 5.2
19 70 75 N 290 290 E 16.3 H-bond
20 72 77 K 120 120 Q 15.7
21 72 77 K 290 290 E 20.8 H-bond, Salt bridge
22 73 78 K 290 290 E 19.2
23 81 86 A 120 120 Q 0.5
24 81 86 A 194 194 A 17.2
25 81 86 A 196 196 N 0.3
26 81 86 A 197 197 V 16.4
27 81 86 A 199 199 T 15.6
28 82 87 F 120 120 Q 11.9
29 82 87 F 196 196 N 2.6
30 82 87 F 197 197 V 11.4
31 83 88 G 120 120 Q 14.9
32 83 88 G 196 196 N 9.8
33 83 88 G 197 197 V 10.3
34 86 91 K 31 31 R 40.2
35 86 91 K 290 290 E 12.2
36 87 92 K 31 31 R 9.3
37 87 92 K 32 32 E 25.9 H-bond
38 87 92 K 34 34 D 19.0 H-bond, Salt bridge
39 90 95 D 34 34 D 10.6
40 90 95 D 39 39 Y 1.9

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A5cid_D201HEM 620.726.4

  • 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_D; 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_D: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

    dssp: -------HHHHHHHHHHH-----E-----------E------------------HHHH--


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    5cid_D: 61 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 108

    dssp: ---------------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_C; 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% (16/16).

    Identities = 100% (16/16), Positive = 100% (16/16), Gaps = 0% (0/16).

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    5cid_C: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    5cid_C: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    5cid_C: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    5cid_C: 181 HLKNSGYEGPGGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    5cid_C: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

    dssp: -HHHHHHHHHHH--HHHHHHHHHHHHHHHHH--EE--------E----------


    Download alignment FASTA file