Interaction between Cytochrome c iso-1 (5cih_B) and Cytochrome c peroxidase, mitochondrial (5cih_A)

PDB and SCOP data

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

Title: Complex of yeast cytochrome c peroxidase (W191Y) with iso-1 cytochrome c

Release date: 2016-08-03

Resolution: 2.6 Å

  • Chain A: 5cih_B

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 103

  • Chain B: 5cih_A

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 518.11 Å2

Number of inter-residue contacts at the interface: 38

Number of H-bonds: 2

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 5cih_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 8 8 T 18.2 22.3 %
    2 9 9 L 28.0 79.4 %
    3 12 12 T 52.8 63.9 %
    4 13 13 R 68.3 75.9 %
    5 16 16 Q 40.1 41.6 %
    6 17 17 C 4.8 97.6 %
    7 28 28 V 23.9 33.8 %
    8 70 70 N 17.7 43.7 %
    9 72 72 K 33.3 31.8 %
    10 73 73 K 27.0 15.9 %
    11 81 81 A 46.7 69.2 %
    12 82 82 F 22.2 76.6 %
    13 83 83 G 24.6 39.2 %
    14 86 86 K 56.3 44.8 %
    15 87 87 K 52.1 41.0 %
    16 90 90 D 2.0 22.0 %

  • Interface residues in 5cih_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 55.5 47.8 %
    2 32 32 E 4.4 3.7 %
    3 34 34 D 48.9 71.8 %
    4 35 35 E 11.7 8.9 %
    5 38 38 N 29.1 23.7 %
    6 39 39 Y 103.0 73.5 %
    7 120 120 Q 43.5 35.0 %
    8 193 193 A 42.7 93.9 %
    9 194 194 A 15.3 82.3 %
    10 195 195 N 13.8 42.1 %
    11 196 196 N 25.5 45.1 %
    12 197 197 V 43.1 94.0 %
    13 199 199 T 12.2 32.4 %
    14 229 229 Y 15.7 44.1 %
    15 290 290 E 48.7 36.7 %
    16 294 294 L 5.2 4.2 %

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 8 8 T 39 39 Y 18.2
2 9 9 L 39 39 Y 28.0
3 12 12 T 38 38 N 29.1
4 12 12 T 39 39 Y 20.2
5 12 12 T 195 195 N 3.5
6 13 13 R 34 34 D 21.5 Salt bridge
7 13 13 R 39 39 Y 31.0
8 13 13 R 196 196 N 15.8
9 16 16 Q 193 193 A 27.2 H-bond
10 16 16 Q 194 194 A 0.2
11 16 16 Q 195 195 N 10.2
12 16 16 Q 229 229 Y 2.4
13 17 17 C 193 193 A 4.8
14 28 28 V 193 193 A 10.7
15 28 28 V 229 229 Y 13.2
16 70 70 N 290 290 E 17.7 H-bond
17 72 72 K 120 120 Q 30.0
18 72 72 K 290 290 E 3.3
19 73 73 K 290 290 E 27.0
20 81 81 A 120 120 Q 0.5
21 81 81 A 194 194 A 15.0
22 81 81 A 197 197 V 19.1
23 81 81 A 199 199 T 12.2
24 82 82 F 120 120 Q 8.2
25 82 82 F 196 196 N 3.8
26 82 82 F 197 197 V 10.3
27 83 83 G 120 120 Q 4.9
28 83 83 G 196 196 N 5.9
29 83 83 G 197 197 V 13.8
30 86 86 K 31 31 R 50.3
31 86 86 K 290 290 E 0.7
32 86 86 K 294 294 L 5.2
33 87 87 K 31 31 R 5.1
34 87 87 K 32 32 E 4.4
35 87 87 K 34 34 D 25.4 Salt bridge
36 87 87 K 35 35 E 11.7
37 87 87 K 39 39 Y 5.5
38 90 90 D 34 34 D 2.0

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A5cih_B201HEM 630.128.3

  • 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: 5cih_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% (16/16).

    Identities = 100% (16/16), Positive = 100% (16/16), Gaps = 0% (0/16).

    Query: 7 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 66

    GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD

    5cih_B: 1 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 60

    dssp: -----HHHHHHHH-----------------------------------------------


    Query: 67 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    5cih_B: 61 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 103

    dssp: HHHHHHHHH-HHHH--------------HHHHHHHHHHH----


    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: 5cih_A; Cytochrome c peroxidase, mitochondrial

    Alignment data:

    Expectation value = 0, Score = 609 bits (1568),

    Identities = 99% (291/294), Positive = 99% (292/294), Gaps = 0% (0/294).

    Interface alignment data:

    Interface residues in alignment: 100% (16/16).

    Identities = 100% (16/16), Positive = 100% (16/16), Gaps = 0% (0/16).

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    5cih_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    5cih_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

    dssp: --E----------------------HHHHHHHHHHH-------HHHHHHHHHHHHHHH--


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    5cih_A: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

    dssp: -----E--------HHH-------------HHHHHHH-------HHHHHHHHHHHH--EE


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP+GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    5cih_A: 181 HLKNSGYEGPYGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    5cih_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

    dssp: -HHHHHHHHHHHH--HHHHHHHHHHHHHHH---EE--------E----------


    Download alignment FASTA file