Interaction between Cytochrome c iso-1 (5cic_B) and Cytochrome c peroxidase, mitochondrial (5cic_A)

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_B

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 108

  • Chain B: 5cic_A

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 514.65 Å2

Number of inter-residue contacts at the interface: 40

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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  • Interface residues in 5cic_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 10 K 17.5 21.6 %
    2 8 13 T 8.1 10.3 %
    3 9 14 L 19.2 99.8 %
    4 12 17 T 49.8 56.5 %
    5 13 18 R 61.7 76.6 %
    6 16 21 Q 41.8 42.8 %
    7 17 22 C 7.6 100.0 %
    8 28 33 V 25.4 28.2 %
    9 70 75 N 23.4 49.5 %
    10 72 77 K 22.6 19.9 %
    11 73 78 K 2.9 1.8 %
    12 81 86 A 47.7 71.2 %
    13 82 87 F 23.5 72.0 %
    14 83 88 G 29.6 50.2 %
    15 85 90 L <0.1 1.7 %
    16 86 91 K 59.4 49.4 %
    17 87 92 K 57.4 49.7 %
    18 90 95 D 17.0 65.0 %

  • Interface residues in 5cic_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 58.3 46.0 %
    2 32 32 E 25.3 17.7 %
    3 34 34 D 49.3 65.9 %
    4 38 38 N 29.7 21.6 %
    5 39 39 Y 102.3 72.6 %
    6 120 120 Q 45.3 37.9 %
    7 193 193 A 49.3 93.9 %
    8 194 194 A 15.2 68.6 %
    9 195 195 N 4.3 20.8 %
    10 196 196 N 25.1 44.7 %
    11 197 197 V 40.1 91.0 %
    12 199 199 T 12.5 36.6 %
    13 201 201 E 1.9 7.7 %
    14 229 229 Y 19.3 46.5 %
    15 290 290 E 27.5 20.6 %
    16 294 294 L 9.2 8.7 %

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 17.5
2 8 13 T 39 39 Y 8.1
3 9 14 L 39 39 Y 19.2
4 12 17 T 38 38 N 29.7
5 12 17 T 39 39 Y 20.1
6 13 18 R 34 34 D 16.0
7 13 18 R 39 39 Y 30.8
8 13 18 R 196 196 N 14.9
9 16 21 Q 193 193 A 29.4
10 16 21 Q 195 195 N 4.3
11 16 21 Q 229 229 Y 8.1
12 17 22 C 193 193 A 7.6
13 28 33 V 193 193 A 12.3
14 28 33 V 201 201 E 1.9
15 28 33 V 229 229 Y 11.2
16 70 75 N 290 290 E 22.8 H-bond
17 70 75 N 294 294 L 0.6
18 72 77 K 120 120 Q 22.3
19 72 77 K 197 197 V 0.3
20 73 78 K 290 290 E 2.9
21 81 86 A 120 120 Q 0.4
22 81 86 A 194 194 A 15.2
23 81 86 A 197 197 V 19.6
24 81 86 A 199 199 T 12.5
25 82 87 F 120 120 Q 12.7
26 82 87 F 196 196 N 2.2
27 82 87 F 197 197 V 8.6
28 83 88 G 120 120 Q 9.9
29 83 88 G 196 196 N 8.0
30 83 88 G 197 197 V 11.6
31 85 90 L 34 34 D <0.1
32 86 91 K 31 31 R 47.7
33 86 91 K 34 34 D 1.4
34 86 91 K 290 290 E 1.8
35 86 91 K 294 294 L 8.5
36 87 92 K 31 31 R 10.6 H-bond
37 87 92 K 32 32 E 25.3 H-bond
38 87 92 K 34 34 D 21.5 Salt bridge
39 90 95 D 34 34 D 10.4
40 90 95 D 39 39 Y 6.6

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A5cic_B201HEM 618.023.2

  • 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: 5cic_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% (18/18).

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

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    5cic_B: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

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


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    5cic_B: 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_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% (16/16).

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

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    5cic_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    5cic_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    5cic_A: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    5cic_A: 181 HLKNSGYEGPGGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    5cic_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file