Interaction between Cytochrome c iso-1 (5cif_B) and Cytochrome c peroxidase, mitochondrial (5cif_A)

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_B

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 103

  • Chain B: 5cif_A

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 548.79 Å2

Number of inter-residue contacts at the interface: 48

Number of H-bonds: 2

  • Pairwise interaction

    Download PDB coordinates

    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 2 proteins.

    Download PDB coordinates


Create a structural model for this interaction

  • Interface residues in 5cif_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 5 K 23.5 27.3 %
    2 8 8 T 13.3 17.7 %
    3 9 9 L 19.5 95.8 %
    4 12 12 T 54.8 61.6 %
    5 13 13 R 63.6 76.5 %
    6 16 16 Q 49.1 52.2 %
    7 17 17 C 5.2 100.0 %
    8 27 27 K 1.7 2.0 %
    9 28 28 V 26.6 32.7 %
    10 70 70 N 26.6 54.2 %
    11 72 72 K 32.4 23.4 %
    12 81 81 A 51.1 70.6 %
    13 82 82 F 19.8 76.5 %
    14 83 83 G 37.1 65.7 %
    15 85 85 L 1.3 45.2 %
    16 86 86 K 63.8 50.5 %
    17 87 87 K 46.8 37.6 %
    18 90 90 D 12.5 62.9 %

  • Interface residues in 5cif_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 59.0 43.8 %
    2 32 32 E 16.6 13.0 %
    3 34 34 D 49.7 71.7 %
    4 35 35 E 12.2 10.1 %
    5 38 38 N 28.7 21.1 %
    6 39 39 Y 102.3 79.6 %
    7 40 40 I <0.1 0.6 %
    8 120 120 Q 62.1 56.1 %
    9 192 192 G 1.5 38.0 %
    10 193 193 A 40.0 92.0 %
    11 194 194 A 18.8 84.9 %
    12 195 195 N 21.2 52.4 %
    13 196 196 N 26.4 47.1 %
    14 197 197 V 39.7 88.4 %
    15 199 199 T 15.0 41.5 %
    16 227 227 S 2.8 5.4 %
    17 229 229 Y 21.9 63.6 %
    18 290 290 E 23.6 18.4 %
    19 294 294 L 7.2 7.7 %

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 5 K 35 35 E 7.2
2 5 5 K 39 39 Y 16.3
3 8 8 T 39 39 Y 13.3
4 9 9 L 34 34 D <0.1
5 9 9 L 39 39 Y 19.5
6 12 12 T 38 38 N 28.7
7 12 12 T 39 39 Y 20.5
8 12 12 T 40 40 I <0.1
9 12 12 T 195 195 N 5.6
10 13 13 R 34 34 D 16.9
11 13 13 R 39 39 Y 29.5
12 13 13 R 196 196 N 17.2
13 16 16 Q 192 192 G 1.5
14 16 16 Q 193 193 A 22.9 H-bond
15 16 16 Q 194 194 A 0.9
16 16 16 Q 195 195 N 15.6
17 16 16 Q 227 227 S 1.1
18 16 16 Q 229 229 Y 7.0
19 17 17 C 193 193 A 5.2
20 27 27 K 227 227 S 1.7
21 28 28 V 193 193 A 11.8
22 28 28 V 229 229 Y 14.8
23 70 70 N 120 120 Q 3.9
24 70 70 N 290 290 E 21.1 H-bond
25 70 70 N 294 294 L 1.6
26 72 72 K 120 120 Q 32.0
27 72 72 K 290 290 E 0.4
28 81 81 A 120 120 Q <0.1
29 81 81 A 194 194 A 17.8
30 81 81 A 197 197 V 18.2
31 81 81 A 199 199 T 15.0
32 82 82 F 120 120 Q 7.8
33 82 82 F 196 196 N 3.1
34 82 82 F 197 197 V 9.0
35 83 83 G 120 120 Q 18.4
36 83 83 G 196 196 N 6.1
37 83 83 G 197 197 V 12.6
38 85 85 L 34 34 D 1.3
39 86 86 K 31 31 R 55.1
40 86 86 K 34 34 D 0.9
41 86 86 K 290 290 E 2.1
42 86 86 K 294 294 L 5.6
43 87 87 K 31 31 R 4.0
44 87 87 K 32 32 E 16.6
45 87 87 K 34 34 D 21.3
46 87 87 K 35 35 E 5.0
47 90 90 D 34 34 D 9.3
48 90 90 D 39 39 Y 3.2

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A5cif_B201HEM 626.723.0

  • 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: 5cif_B; 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_B: 1 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 60

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


    Query: 67 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    5cif_B: 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_A; 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% (19/19).

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

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    5cif_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    5cif_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    5cif_A: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP+GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    5cif_A: 181 HLKNSGYEGPFGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    5cif_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file