Interaction between Cytochrome c iso-1 (5cig_B) and Cytochrome c peroxidase, mitochondrial (5cig_A)

PDB and SCOP data

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

Title: Complex of yeast cytochrome c peroxidase (W191G) with iso-1 cytochrome c

Release date: 2016-08-03

Resolution: 2.1 Å

  • Chain A: 5cig_B

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 108

  • Chain B: 5cig_A

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 570.51 Å2

Number of inter-residue contacts at the interface: 46

Number of H-bonds: 3

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 5cig_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 10 K 24.2 25.8 %
    2 8 13 T 9.0 14.5 %
    3 9 14 L 20.3 96.9 %
    4 11 16 K 4.2 3.7 %
    5 12 17 T 48.5 67.4 %
    6 13 18 R 67.1 74.9 %
    7 16 21 Q 42.6 42.7 %
    8 17 22 C 6.9 100.0 %
    9 28 33 V 23.5 27.0 %
    10 70 75 N 19.5 48.2 %
    11 72 77 K 18.6 15.4 %
    12 73 78 K 37.8 23.2 %
    13 81 86 A 47.7 70.9 %
    14 82 87 F 22.4 76.2 %
    15 83 88 G 33.7 57.4 %
    16 86 91 K 65.1 51.7 %
    17 87 92 K 56.8 45.7 %
    18 90 95 D 22.5 81.9 %

  • Interface residues in 5cig_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 57.4 47.1 %
    2 32 32 E 21.8 18.4 %
    3 34 34 D 48.4 71.9 %
    4 35 35 E 28.5 25.4 %
    5 38 38 N 30.5 22.1 %
    6 39 39 Y 100.3 78.8 %
    7 120 120 Q 47.4 41.7 %
    8 193 193 A 49.9 93.4 %
    9 194 194 A 12.2 64.0 %
    10 195 195 N 6.6 31.5 %
    11 196 196 N 29.5 48.1 %
    12 197 197 V 36.2 89.0 %
    13 199 199 T 13.0 36.8 %
    14 201 201 E 0.5 2.4 %
    15 229 229 Y 15.9 39.2 %
    16 255 255 Q 0.5 0.8 %
    17 290 290 E 58.4 46.5 %
    18 293 293 G 0.3 0.4 %
    19 294 294 L 13.2 11.9 %

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 13.5 Salt bridge
2 5 10 K 39 39 Y 10.7
3 8 13 T 39 39 Y 9.0
4 9 14 L 39 39 Y 20.3
5 11 16 K 38 38 N 3.9
6 11 16 K 39 39 Y 0.3
7 12 17 T 38 38 N 26.6
8 12 17 T 39 39 Y 21.9
9 13 18 R 34 34 D 18.2
10 13 18 R 39 39 Y 32.7
11 13 18 R 196 196 N 16.3
12 16 21 Q 193 193 A 32.1
13 16 21 Q 195 195 N 6.6
14 16 21 Q 229 229 Y 3.9
15 17 22 C 193 193 A 6.9
16 28 33 V 193 193 A 11.0
17 28 33 V 201 201 E 0.5
18 28 33 V 229 229 Y 12.0
19 70 75 N 290 290 E 19.5 H-bond
20 72 77 K 120 120 Q 18.2
21 72 77 K 255 255 Q 0.5
22 73 78 K 290 290 E 32.4
23 73 78 K 293 293 G 0.3
24 73 78 K 294 294 L 5.0
25 81 86 A 120 120 Q 0.7
26 81 86 A 194 194 A 12.2
27 81 86 A 196 196 N 0.2
28 81 86 A 197 197 V 21.7
29 81 86 A 199 199 T 13.0
30 82 87 F 120 120 Q 11.0
31 82 87 F 196 196 N 4.9
32 82 87 F 197 197 V 6.4
33 83 88 G 120 120 Q 17.5
34 83 88 G 196 196 N 8.1
35 83 88 G 197 197 V 8.1
36 86 91 K 31 31 R 49.0
37 86 91 K 34 34 D 1.3
38 86 91 K 290 290 E 6.5
39 86 91 K 294 294 L 8.2
40 87 92 K 31 31 R 8.4
41 87 92 K 32 32 E 21.8 H-bond
42 87 92 K 34 34 D 18.4 H-bond, Salt bridge
43 87 92 K 35 35 E 8.2
44 90 95 D 34 34 D 10.4
45 90 95 D 35 35 E 6.7
46 90 95 D 39 39 Y 5.3

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A5cig_B201HEM 629.924.0

  • 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: 5cig_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

    5cig_B: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

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


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    5cig_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: 5cig_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% (19/19).

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

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    5cig_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    5cig_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    5cig_A: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

    dssp: -----E--------HHH-------------HHHHHHHHHHH---HHHHHHHHHHHH--EE


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    5cig_A: 181 HLKNSGYEGPGGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    5cig_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file