Interaction between Cytochrome c iso-1 (5cie_D) and Cytochrome c peroxidase, mitochondrial (5cie_C)

PDB and SCOP data

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

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

Release date: 2016-08-03

Resolution: 2.6 Å

  • Chain A: 5cie_D

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 108

  • Chain B: 5cie_C

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 518.26 Å2

Number of inter-residue contacts at the interface: 40

Number of H-bonds: 5

Number of salt bridges: 2

  • 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 5cie_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 10 K 28.3 26.4 %
    2 8 13 T 5.3 7.4 %
    3 9 14 L 23.4 85.6 %
    4 12 17 T 43.6 54.9 %
    5 13 18 R 57.9 71.8 %
    6 16 21 Q 29.8 32.0 %
    7 17 22 C 7.8 100.0 %
    8 28 33 V 25.8 34.0 %
    9 70 75 N 26.4 59.6 %
    10 71 76 P 1.3 21.9 %
    11 72 77 K 9.6 9.8 %
    12 73 78 K 25.6 18.3 %
    13 81 86 A 41.4 59.8 %
    14 82 87 F 31.2 86.8 %
    15 83 88 G 32.3 57.9 %
    16 86 91 K 41.6 33.6 %
    17 87 92 K 54.2 54.4 %
    18 89 94 K 20.1 17.7 %
    19 90 95 D 12.6 85.0 %

  • Interface residues in 5cie_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 53.4 46.3 %
    2 32 32 E 23.0 20.3 %
    3 34 34 D 45.6 69.6 %
    4 35 35 E 19.9 16.5 %
    5 38 38 N 27.6 20.1 %
    6 39 39 Y 103.5 83.3 %
    7 120 120 Q 47.3 38.6 %
    8 193 193 A 46.0 87.3 %
    9 194 194 A 11.7 68.9 %
    10 196 196 N 34.6 52.3 %
    11 197 197 V 35.9 87.3 %
    12 199 199 T 9.9 34.2 %
    13 201 201 E 0.6 2.6 %
    14 229 229 Y 16.8 45.3 %
    15 290 290 E 42.5 32.2 %

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 6.8
2 5 10 K 39 39 Y 21.5 H-bond
3 8 13 T 39 39 Y 5.3
4 9 14 L 39 39 Y 23.4
5 12 17 T 38 38 N 27.6
6 12 17 T 39 39 Y 15.9
7 13 18 R 34 34 D 14.9
8 13 18 R 39 39 Y 28.9
9 13 18 R 196 196 N 14.1
10 16 21 Q 193 193 A 25.3
11 16 21 Q 229 229 Y 4.4
12 17 22 C 193 193 A 7.8
13 28 33 V 193 193 A 12.8
14 28 33 V 201 201 E 0.6
15 28 33 V 229 229 Y 12.3
16 70 75 N 120 120 Q 9.5
17 70 75 N 290 290 E 16.8
18 71 76 P 120 120 Q 1.3
19 72 77 K 120 120 Q 9.6
20 73 78 K 290 290 E 25.6 H-bond, Salt bridge
21 81 86 A 120 120 Q 0.6
22 81 86 A 194 194 A 11.7
23 81 86 A 197 197 V 19.1
24 81 86 A 199 199 T 9.9
25 82 87 F 120 120 Q 12.5 H-bond
26 82 87 F 196 196 N 8.0
27 82 87 F 197 197 V 10.7
28 83 88 G 120 120 Q 13.8
29 83 88 G 196 196 N 12.4
30 83 88 G 197 197 V 6.1
31 86 91 K 31 31 R 41.6
32 87 92 K 31 31 R 11.7
33 87 92 K 32 32 E 23.0 H-bond
34 87 92 K 34 34 D 18.9 H-bond, Salt bridge
35 87 92 K 35 35 E 0.6
36 89 94 K 34 34 D 2.8
37 89 94 K 35 35 E 12.5
38 89 94 K 39 39 Y 4.8
39 90 95 D 34 34 D 9.1
40 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
A5cie_D201HEM 630.824.4

  • 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: 5cie_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% (19/19).

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

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    5cie_D: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

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


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    5cie_D: 61 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 108

    dssp: --------HHHH--------------------HHHHHHHHHHHHH---


    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: 5cie_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% (15/15).

    Identities = 100% (15/15), Positive = 100% (15/15), Gaps = 0% (0/15).

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    5cie_C: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    5cie_C: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

    dssp: --E-----------HHHH-------HHHHHHHHHHHH------HHHHHHHHHHHHHHH--


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    5cie_C: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    5cie_C: 181 HLKNSGYEGPGGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

    dssp: -HHHH---EE----------HHHHHHHH---EEEE-----EEEE-----EE-HHHH----


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    5cie_C: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

    dssp: -HHHHHHHHHHHH-HHHHHHHHHHHHHHHH---EE--------E-----HHH--


    Download alignment FASTA file