Interaction between Cytochrome c iso-1 (4p4q_B) and Cytochrome c peroxidase, mitochondrial (4p4q_A)

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_B

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae

    Number of residues: 103

  • Chain B: 4p4q_A

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae

    Number of residues: 294

Buried interface area: 550.88 Å2

Number of inter-residue contacts at the interface: 46

Number of H-bonds: 3

  • 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_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 5 K 24.0 27.8 %
    2 8 8 T 13.1 17.2 %
    3 9 9 L 19.0 96.0 %
    4 12 12 T 53.7 59.7 %
    5 13 13 R 63.3 75.3 %
    6 16 16 Q 49.2 51.1 %
    7 17 17 C 7.9 100.0 %
    8 28 28 V 27.6 33.2 %
    9 70 70 N 26.2 53.9 %
    10 72 72 K 32.6 23.3 %
    11 81 81 A 48.6 70.7 %
    12 82 82 F 20.9 75.0 %
    13 83 83 G 36.8 66.3 %
    14 85 85 L 1.1 39.4 %
    15 86 86 K 55.3 50.2 %
    16 87 87 K 56.2 50.9 %
    17 90 90 D 15.4 55.7 %

  • Interface residues in 4p4q_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 64.7 47.7 %
    2 32 32 E 18.5 14.2 %
    3 34 34 D 49.2 68.4 %
    4 35 35 E 7.8 6.6 %
    5 38 38 N 28.7 21.0 %
    6 39 39 Y 101.1 79.7 %
    7 120 120 Q 63.1 56.1 %
    8 192 192 G 1.5 39.1 %
    9 193 193 A 41.5 92.1 %
    10 194 194 A 16.7 84.7 %
    11 195 195 N 21.8 52.3 %
    12 196 196 N 26.2 47.2 %
    13 197 197 V 39.7 87.2 %
    14 199 199 T 15.1 42.4 %
    15 227 227 S 1.7 3.1 %
    16 229 229 Y 22.5 66.7 %
    17 290 290 E 23.5 18.6 %
    18 294 294 L 7.7 8.4 %

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 7.8
2 5 5 K 39 39 Y 16.2
3 8 8 T 39 39 Y 13.1
4 9 9 L 34 34 D 0.1
5 9 9 L 39 39 Y 18.9
6 12 12 T 38 38 N 28.7
7 12 12 T 39 39 Y 19.9
8 12 12 T 195 195 N 5.1
9 13 13 R 34 34 D 16.6
10 13 13 R 39 39 Y 29.6
11 13 13 R 196 196 N 17.0
12 16 16 Q 192 192 G 1.5
13 16 16 Q 193 193 A 21.7 H-bond
14 16 16 Q 194 194 A 0.9
15 16 16 Q 195 195 N 16.7
16 16 16 Q 227 227 S 1.7
17 16 16 Q 229 229 Y 6.8
18 17 17 C 193 193 A 7.9
19 28 28 V 193 193 A 11.9
20 28 28 V 227 227 S <0.1
21 28 28 V 229 229 Y 15.7
22 70 70 N 120 120 Q 4.0
23 70 70 N 290 290 E 20.7 H-bond
24 70 70 N 294 294 L 1.5
25 72 72 K 120 120 Q 32.5
26 72 72 K 290 290 E 0.1
27 81 81 A 120 120 Q <0.1
28 81 81 A 194 194 A 15.8
29 81 81 A 197 197 V 17.7
30 81 81 A 199 199 T 15.1
31 82 82 F 120 120 Q 8.0
32 82 82 F 196 196 N 3.4
33 82 82 F 197 197 V 9.5
34 83 83 G 120 120 Q 18.6
35 83 83 G 196 196 N 5.8
36 83 83 G 197 197 V 12.5
37 85 85 L 34 34 D 1.1
38 86 86 K 31 31 R 46.1
39 86 86 K 34 34 D 0.3
40 86 86 K 290 290 E 2.7
41 86 86 K 294 294 L 6.2
42 87 87 K 31 31 R 18.6 H-bond
43 87 87 K 32 32 E 18.5
44 87 87 K 34 34 D 19.1
45 90 90 D 34 34 D 12.0
46 90 90 D 39 39 Y 3.5

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A4p4q_B201HEM 622.223.0

  • 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: 4p4q_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% (17/17).

    Identities = 100% (17/17), Positive = 100% (17/17), Gaps = 0% (0/17).

    Query: 7 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 66

    GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD

    4p4q_B: 1 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 60

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


    Query: 67 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    4p4q_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: 4p4q_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% (18/18).

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

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    4p4q_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    4p4q_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    4p4q_A: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP+GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    4p4q_A: 181 HLKNSGYEGPFGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    4p4q_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file