Interaction between Cytochrome c iso-1 (5cib_B) and Cytochrome c peroxidase, mitochondrial (5cib_A)

PDB and SCOP data

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

Title: Complex of yeast cytochrome c peroxidase (W191G) bound to 2,4-dimethylaniline with iso-1 cytochrome c

Release date: 2016-08-03

Resolution: 3.0 Å

  • Chain A: 5cib_B

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 108

  • Chain B: 5cib_A

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 519.42 Å2

Number of inter-residue contacts at the interface: 41

Number of salt bridges: 3

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 4 proteins.

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Create a structural model for this interaction

  • Interface residues in 5cib_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 8 13 T 10.7 16.1 %
    2 9 14 L 25.4 80.7 %
    3 11 16 K 8.4 6.8 %
    4 12 17 T 54.1 75.1 %
    5 13 18 R 60.9 73.7 %
    6 16 21 Q 29.9 32.9 %
    7 17 22 C 7.4 100.0 %
    8 28 33 V 26.4 29.0 %
    9 70 75 N 20.9 43.8 %
    10 72 77 K 56.2 40.8 %
    11 73 78 K 7.6 4.8 %
    12 81 86 A 45.2 63.5 %
    13 82 87 F 23.9 75.0 %
    14 83 88 G 32.1 53.8 %
    15 85 90 L <0.1 0.0 %
    16 86 91 K 48.6 40.0 %
    17 87 92 K 49.9 48.0 %
    18 90 95 D 12.0 32.8 %

  • Interface residues in 5cib_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 58.3 50.9 %
    2 32 32 E 17.5 16.7 %
    3 34 34 D 42.6 64.6 %
    4 35 35 E 0.7 0.6 %
    5 38 38 N 36.4 27.5 %
    6 39 39 Y 88.8 64.5 %
    7 40 40 I 7.6 27.0 %
    8 120 120 Q 55.4 48.7 %
    9 193 193 A 45.1 86.8 %
    10 194 194 A 15.9 75.2 %
    11 195 195 N 2.3 14.0 %
    12 196 196 N 25.5 47.0 %
    13 197 197 V 37.1 91.3 %
    14 199 199 T 11.9 33.1 %
    15 201 201 E 0.8 2.8 %
    16 229 229 Y 13.3 36.7 %
    17 290 290 E 53.1 41.3 %
    18 294 294 L 7.1 6.6 %

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 8 13 T 39 39 Y 10.7
2 9 14 L 39 39 Y 25.4
3 11 16 K 38 38 N 8.4
4 12 17 T 38 38 N 28.0
5 12 17 T 39 39 Y 20.7
6 12 17 T 40 40 I 5.4
7 13 18 R 34 34 D 15.8 Salt bridge
8 13 18 R 39 39 Y 30.0
9 13 18 R 196 196 N 15.1
10 16 21 Q 40 40 I 2.3
11 16 21 Q 193 193 A 24.8
12 16 21 Q 195 195 N 2.3
13 16 21 Q 229 229 Y 0.4
14 17 22 C 193 193 A 7.4
15 28 33 V 193 193 A 12.8
16 28 33 V 201 201 E 0.8
17 28 33 V 229 229 Y 12.8
18 70 75 N 290 290 E 18.9
19 70 75 N 294 294 L 2.0
20 72 77 K 120 120 Q 29.5
21 72 77 K 290 290 E 26.6 Salt bridge
22 73 78 K 290 290 E 7.6
23 81 86 A 120 120 Q 0.4
24 81 86 A 194 194 A 15.9
25 81 86 A 197 197 V 16.9
26 81 86 A 199 199 T 11.9
27 82 87 F 120 120 Q 11.0
28 82 87 F 196 196 N 3.6
29 82 87 F 197 197 V 9.3
30 83 88 G 120 120 Q 14.5
31 83 88 G 196 196 N 6.8
32 83 88 G 197 197 V 10.9
33 85 90 L 34 34 D <0.1
34 86 91 K 31 31 R 43.5
35 86 91 K 294 294 L 5.1
36 87 92 K 31 31 R 14.8
37 87 92 K 32 32 E 17.5
38 87 92 K 34 34 D 16.9 Salt bridge
39 87 92 K 35 35 E 0.7
40 90 95 D 34 34 D 9.9
41 90 95 D 39 39 Y 2.1

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A5cib_B201HEM 632.224.0

  • 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: 5cib_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

    5cib_B: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

    dssp: ------------HHHHHH-------------------------E----------HHHHH-


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    5cib_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: 5cib_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% (18/18).

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

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    5cib_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    5cib_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    5cib_A: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    5cib_A: 181 HLKNSGYEGPGGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    5cib_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file