Interaction between Cytochrome c iso-1 (5cif_D) and Cytochrome c peroxidase, mitochondrial (5cif_C)

PDB and SCOP data

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

Title: Complex of yeast cytochrome c peroxidase (W191F) with iso-1 cytochrome c

Release date: 2016-08-03

Resolution: 2.0 Å

  • Chain A: 5cif_D

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 103

  • Chain B: 5cif_C

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 533.93 Å2

Number of inter-residue contacts at the interface: 43

Number of H-bonds: 2

Number of salt bridges: 1

  • 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 5cif_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 5 K 20.2 23.0 %
    2 8 8 T 10.3 14.1 %
    3 9 9 L 20.6 97.7 %
    4 12 12 T 57.5 60.1 %
    5 13 13 R 67.0 80.4 %
    6 16 16 Q 48.3 51.3 %
    7 17 17 C 6.2 100.0 %
    8 27 27 K 0.9 1.0 %
    9 28 28 V 25.2 30.9 %
    10 70 70 N 13.5 31.3 %
    11 72 72 K 52.9 36.1 %
    12 81 81 A 50.6 71.7 %
    13 82 82 F 19.5 66.2 %
    14 83 83 G 29.1 49.9 %
    15 85 85 L 0.4 32.0 %
    16 86 86 K 50.6 41.7 %
    17 87 87 K 46.4 37.7 %
    18 90 90 D 14.6 70.7 %

  • Interface residues in 5cif_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 50.1 36.0 %
    2 32 32 E 14.6 14.8 %
    3 34 34 D 57.5 77.0 %
    4 35 35 E 14.4 11.9 %
    5 38 38 N 29.3 21.1 %
    6 39 39 Y 102.0 78.5 %
    7 120 120 Q 56.5 55.1 %
    8 192 192 G 0.6 20.5 %
    9 193 193 A 41.4 93.9 %
    10 194 194 A 18.7 82.5 %
    11 195 195 N 18.0 47.5 %
    12 196 196 N 25.9 47.9 %
    13 197 197 V 38.4 86.6 %
    14 199 199 T 13.4 34.7 %
    15 227 227 S 1.1 1.8 %
    16 229 229 Y 23.5 67.5 %
    17 290 290 E 28.6 23.1 %

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 5 K 35 35 E 7.4
2 5 5 K 39 39 Y 12.8
3 8 8 T 39 39 Y 10.3
4 9 9 L 39 39 Y 20.6
5 12 12 T 38 38 N 29.3
6 12 12 T 39 39 Y 24.1
7 12 12 T 195 195 N 4.2
8 13 13 R 34 34 D 20.6
9 13 13 R 39 39 Y 30.9
10 13 13 R 196 196 N 15.5
11 16 16 Q 192 192 G 0.6
12 16 16 Q 193 193 A 24.7 H-bond
13 16 16 Q 194 194 A 0.2
14 16 16 Q 195 195 N 13.8
15 16 16 Q 227 227 S 0.3
16 16 16 Q 229 229 Y 8.8
17 17 17 C 193 193 A 6.2
18 27 27 K 227 227 S 0.9
19 28 28 V 193 193 A 10.4
20 28 28 V 229 229 Y 14.8
21 70 70 N 120 120 Q 3.4
22 70 70 N 290 290 E 10.1
23 72 72 K 120 120 Q 34.5
24 72 72 K 290 290 E 18.4
25 81 81 A 120 120 Q 0.2
26 81 81 A 194 194 A 18.5
27 81 81 A 197 197 V 18.5
28 81 81 A 199 199 T 13.4
29 82 82 F 120 120 Q 9.3
30 82 82 F 196 196 N 2.1
31 82 82 F 197 197 V 8.2
32 83 83 G 120 120 Q 9.1
33 83 83 G 196 196 N 8.3
34 83 83 G 197 197 V 11.7
35 85 85 L 34 34 D 0.4
36 86 86 K 31 31 R 47.7
37 86 86 K 34 34 D 3.0
38 87 87 K 31 31 R 2.4
39 87 87 K 32 32 E 14.6
40 87 87 K 34 34 D 22.4 H-bond, Salt bridge
41 87 87 K 35 35 E 7.0
42 90 90 D 34 34 D 11.2
43 90 90 D 39 39 Y 3.4

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A5cif_D201HEM 620.522.9

  • 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: 5cif_D; Cytochrome c iso-1

    Alignment data:

    Expectation value = 6.80e-74, Score = 216 bits (550),

    Identities = 100% (103/103), Positive = 100% (103/103), Gaps = 0% (0/103).

    Interface alignment data:

    Interface residues in alignment: 100% (18/18).

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

    Query: 7 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 66

    GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD

    5cif_D: 1 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 60

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


    Query: 67 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    5cif_D: 61 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 103

    dssp: 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: 5cif_C; Cytochrome c peroxidase, mitochondrial

    Alignment data:

    Expectation value = 0, Score = 608 bits (1567),

    Identities = 99% (291/294), Positive = 99% (292/294), 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

    5cif_C: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    5cif_C: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    5cif_C: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP+GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    5cif_C: 181 HLKNSGYEGPFGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    5cif_C: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file