Interaction between Cytochrome c iso-1 (4p4q_D) and Cytochrome c peroxidase, mitochondrial (4p4q_C)

PDB and SCOP data

PDB ID: 4p4q (all binary interactions in this PDB entry)

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

Release date: 2015-03-25

Resolution: 2.0 Å

  • Chain A: 4p4q_D

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae

    Number of residues: 103

  • Chain B: 4p4q_C

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae

    Number of residues: 294

Buried interface area: 495.91 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 4p4q_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 5 K 15.6 17.8 %
    2 8 8 T 8.9 12.4 %
    3 9 9 L 19.5 98.5 %
    4 12 12 T 55.6 56.6 %
    5 13 13 R 67.0 79.8 %
    6 16 16 Q 49.9 52.3 %
    7 17 17 C 8.5 100.0 %
    8 27 27 K 2.2 2.5 %
    9 28 28 V 26.7 32.1 %
    10 70 70 N 13.5 26.6 %
    11 72 72 K 17.5 14.0 %
    12 81 81 A 47.7 72.2 %
    13 82 82 F 19.3 66.0 %
    14 83 83 G 28.8 49.5 %
    15 85 85 L 0.6 45.8 %
    16 86 86 K 49.5 41.0 %
    17 87 87 K 50.1 40.9 %
    18 90 90 D 15.2 69.3 %

  • Interface residues in 4p4q_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 49.0 35.5 %
    2 32 32 E 13.8 14.1 %
    3 34 34 D 56.8 77.2 %
    4 35 35 E 9.9 7.9 %
    5 38 38 N 29.2 21.1 %
    6 39 39 Y 103.9 75.1 %
    7 120 120 Q 39.5 36.7 %
    8 192 192 G 1.0 29.5 %
    9 193 193 A 43.5 94.5 %
    10 194 194 A 16.6 85.3 %
    11 195 195 N 18.8 48.4 %
    12 196 196 N 25.7 47.4 %
    13 197 197 V 38.7 86.0 %
    14 199 199 T 13.0 34.6 %
    15 227 227 S 2.9 4.7 %
    16 229 229 Y 24.5 69.1 %
    17 290 290 E 9.0 7.3 %

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 39 39 Y 15.6
2 8 8 T 39 39 Y 8.9
3 9 9 L 39 39 Y 19.5
4 12 12 T 38 38 N 29.2
5 12 12 T 39 39 Y 22.8
6 12 12 T 195 195 N 3.6
7 13 13 R 34 34 D 19.4
8 13 13 R 39 39 Y 31.8
9 13 13 R 196 196 N 15.8
10 16 16 Q 192 192 G 1.0
11 16 16 Q 193 193 A 23.5 H-bond
12 16 16 Q 194 194 A 0.1
13 16 16 Q 195 195 N 15.2
14 16 16 Q 227 227 S 0.2
15 16 16 Q 229 229 Y 9.9
16 17 17 C 193 193 A 8.5
17 27 27 K 227 227 S 2.2
18 28 28 V 193 193 A 11.6
19 28 28 V 227 227 S 0.5
20 28 28 V 229 229 Y 14.6
21 70 70 N 120 120 Q 4.5
22 70 70 N 290 290 E 9.0
23 72 72 K 120 120 Q 17.5
24 81 81 A 120 120 Q <0.1
25 81 81 A 194 194 A 16.5
26 81 81 A 197 197 V 18.1
27 81 81 A 199 199 T 13.0
28 82 82 F 120 120 Q 8.3
29 82 82 F 196 196 N 2.1
30 82 82 F 197 197 V 8.8
31 83 83 G 120 120 Q 9.1
32 83 83 G 196 196 N 7.8
33 83 83 G 197 197 V 11.8
34 85 85 L 34 34 D 0.6
35 86 86 K 31 31 R 46.2
36 86 86 K 34 34 D 3.2
37 87 87 K 31 31 R 2.8
38 87 87 K 32 32 E 13.8
39 87 87 K 34 34 D 23.0 H-bond, Salt bridge
40 87 87 K 35 35 E 9.9
41 87 87 K 39 39 Y 0.6
42 90 90 D 34 34 D 10.6
43 90 90 D 39 39 Y 4.6

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A4p4q_D201HEM 614.322.1

  • 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: 4p4q_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

    4p4q_D: 1 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 60

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


    Query: 67 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    4p4q_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: 4p4q_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

    4p4q_C: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    4p4q_C: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    4p4q_C: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP+GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    4p4q_C: 181 HLKNSGYEGPFGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    4p4q_C: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file