Interaction between Cytochrome c iso-1 (5cic_D) and Cytochrome c peroxidase, mitochondrial (5cic_C)

PDB and SCOP data

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

Title: Complex of yeast cytochrome c peroxidase (W191G) bound to 3-aminobenzotrifluoride with iso-1 cytochrome c

Release date: 2016-08-03

Resolution: 2.1 Å

  • Chain A: 5cic_D

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 108

  • Chain B: 5cic_C

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 497.72 Å2

Number of inter-residue contacts at the interface: 39

Number of H-bonds: 3

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 5cic_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 10 K 22.2 27.2 %
    2 8 13 T 7.5 10.9 %
    3 9 14 L 19.5 96.3 %
    4 11 16 K 1.5 1.2 %
    5 12 17 T 50.6 65.5 %
    6 13 18 R 63.8 76.7 %
    7 16 21 Q 40.0 40.1 %
    8 17 22 C 7.5 100.0 %
    9 28 33 V 23.0 25.3 %
    10 70 75 N 22.3 47.0 %
    11 72 77 K 21.4 17.5 %
    12 73 78 K 3.7 2.3 %
    13 81 86 A 50.2 74.3 %
    14 82 87 F 20.8 70.3 %
    15 83 88 G 30.6 53.6 %
    16 86 91 K 42.2 35.8 %
    17 87 92 K 55.5 42.5 %
    18 90 95 D 15.3 55.0 %

  • Interface residues in 5cic_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 47.3 38.8 %
    2 32 32 E 27.1 24.5 %
    3 34 34 D 49.7 71.6 %
    4 35 35 E 11.9 10.0 %
    5 38 38 N 28.3 20.3 %
    6 39 39 Y 100.2 77.3 %
    7 120 120 Q 43.3 36.7 %
    8 193 193 A 49.4 92.5 %
    9 194 194 A 14.5 64.4 %
    10 195 195 N 3.1 15.5 %
    11 196 196 N 22.9 42.3 %
    12 197 197 V 40.3 91.0 %
    13 199 199 T 13.0 36.4 %
    14 201 201 E 1.5 5.9 %
    15 229 229 Y 16.5 38.7 %
    16 255 255 Q 2.1 3.3 %
    17 290 290 E 26.6 17.5 %

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 9.0
2 5 10 K 39 39 Y 13.3
3 8 13 T 39 39 Y 7.5
4 9 14 L 39 39 Y 19.5
5 11 16 K 38 38 N 1.5
6 12 17 T 38 38 N 26.7
7 12 17 T 39 39 Y 23.9
8 13 18 R 34 34 D 18.3
9 13 18 R 39 39 Y 32.4
10 13 18 R 196 196 N 13.1
11 16 21 Q 193 193 A 29.9
12 16 21 Q 195 195 N 3.1
13 16 21 Q 229 229 Y 6.9
14 17 22 C 193 193 A 7.5
15 28 33 V 193 193 A 11.9
16 28 33 V 201 201 E 1.5
17 28 33 V 229 229 Y 9.6
18 70 75 N 290 290 E 22.3 H-bond
19 72 77 K 120 120 Q 19.2
20 72 77 K 255 255 Q 2.1
21 73 78 K 290 290 E 3.7
22 81 86 A 120 120 Q 1.9
23 81 86 A 194 194 A 14.5
24 81 86 A 197 197 V 20.9
25 81 86 A 199 199 T 13.0
26 82 87 F 120 120 Q 9.3
27 82 87 F 196 196 N 3.4
28 82 87 F 197 197 V 8.1
29 83 88 G 120 120 Q 12.8
30 83 88 G 196 196 N 6.4
31 83 88 G 197 197 V 11.4
32 86 91 K 31 31 R 41.7
33 86 91 K 290 290 E 0.5
34 87 92 K 31 31 R 5.7
35 87 92 K 32 32 E 27.1 H-bond
36 87 92 K 34 34 D 19.7 H-bond, Salt bridge
37 87 92 K 35 35 E 3.0
38 90 95 D 34 34 D 11.7
39 90 95 D 39 39 Y 3.6

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A5cic_D201HEM 630.823.1

  • 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: 5cic_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% (18/18).

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

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    5cic_D: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

    dssp: -------HHHHHHHHHHH-------------------------E----------HHHHHH


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    5cic_D: 61 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 108

    dssp: --E--HHHHHHHHH-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: 5cic_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% (17/17).

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

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    5cic_C: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    5cic_C: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    5cic_C: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    5cic_C: 181 HLKNSGYEGPGGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    5cic_C: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file