Interaction between Mitochondrial cytochrome c (1u74_B) and Cytochrome c peroxidase, CCP (1u74_A)

PDB and SCOP data

PDB ID: 1u74 (all binary interactions in this PDB entry)

Title: Electron Transfer Complex between cytochrome C and cytochrome C peroxidase

Release date: 2004-09-28

Resolution: 2.4 Å

  • Chain A: 1u74_B

    Title: Mitochondrial cytochrome c

    Source organism: Saccharomyces cerevisiae

    Number of residues: 108

    SCOP family: a.3.1.1

  • Chain B: 1u74_A

    Title: Cytochrome c peroxidase, CCP

    Source organism: Saccharomyces cerevisiae

    Number of residues: 296 (2 missing in structure)

    SCOP family: a.93.1.1

Buried interface area: 536.92 Å2

Number of inter-residue contacts at the interface: 43

Number of H-bonds: 2

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 2 proteins, 2 domains.

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Create a structural model for this interaction

  • Interface residues in 1u74_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 13 13 T 10.7 17.3 %
    2 14 14 L 24.2 82.6 %
    3 16 16 K 0.2 0.2 %
    4 17 17 T 53.2 70.5 %
    5 18 18 R 64.1 74.6 %
    6 21 21 Q 47.9 49.7 %
    7 22 22 C 7.7 100.0 %
    8 32 32 K 2.3 2.5 %
    9 33 33 V 25.8 30.4 %
    10 75 75 N 25.8 58.1 %
    11 77 77 K 26.4 27.5 %
    12 78 78 K 11.7 7.1 %
    13 86 86 A 49.2 79.4 %
    14 87 87 F 19.4 82.3 %
    15 88 88 G 32.8 54.3 %
    16 90 90 L 0.2 12.7 %
    17 91 91 K 56.4 50.2 %
    18 92 92 K 60.7 53.1 %
    19 95 95 D 18.1 39.8 %

  • Interface residues in 1u74_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 33 R 64.5 54.8 %
    2 32 34 E 19.4 15.8 %
    3 34 36 D 47.4 70.1 %
    4 38 40 N 32.2 22.3 %
    5 39 41 Y 92.9 66.7 %
    6 120 122 Q 47.2 42.2 %
    7 193 195 A 42.7 96.4 %
    8 194 196 A 15.3 79.2 %
    9 195 197 N 15.3 45.8 %
    10 196 198 N 31.4 54.9 %
    11 197 199 V 36.3 94.9 %
    12 199 201 T 15.3 38.7 %
    13 201 203 E 4.3 17.2 %
    14 227 229 S 2.3 4.4 %
    15 229 231 Y 20.4 55.7 %
    16 290 292 E 37.2 26.9 %
    17 294 296 L 12.7 11.5 %

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 13 13 T 39 41 Y 10.7
2 14 14 L 39 41 Y 24.2
3 16 16 K 38 40 N 0.2
4 17 17 T 38 40 N 32.1
5 17 17 T 39 41 Y 19.9
6 17 17 T 195 197 N 1.2
7 18 18 R 34 36 D 17.1
8 18 18 R 39 41 Y 30.4
9 18 18 R 196 198 N 16.6
10 21 21 Q 193 195 A 27.1
11 21 21 Q 195 197 N 14.0
12 21 21 Q 229 231 Y 6.8
13 22 22 C 193 195 A 7.7
14 32 32 K 227 229 S 2.3
15 33 33 V 193 195 A 7.8
16 33 33 V 201 203 E 4.3
17 33 33 V 229 231 Y 13.6
18 75 75 N 120 122 Q 1.0
19 75 75 N 290 292 E 24.2 H-bond
20 75 75 N 294 296 L 0.5
21 77 77 K 120 122 Q 23.8 H-bond
22 77 77 K 197 199 V 2.6
23 78 78 K 290 292 E 11.7
24 86 86 A 194 196 A 15.3
25 86 86 A 196 198 N <0.1
26 86 86 A 197 199 V 18.6
27 86 86 A 199 201 T 15.3
28 87 87 F 120 122 Q 6.8
29 87 87 F 196 198 N 5.0
30 87 87 F 197 199 V 7.6
31 88 88 G 120 122 Q 15.6
32 88 88 G 196 198 N 9.7
33 88 88 G 197 199 V 7.5
34 90 90 L 34 36 D 0.2
35 91 91 K 31 33 R 42.1
36 91 91 K 34 36 D 0.7
37 91 91 K 290 292 E 1.4
38 91 91 K 294 296 L 12.2
39 92 92 K 31 33 R 22.4
40 92 92 K 32 34 E 19.4
41 92 92 K 34 36 D 18.9
42 95 95 D 34 36 D 10.5
43 95 95 D 39 41 Y 7.7

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A1u74_B1101HEM 624.826.5

  • 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: 1u74_B; Mitochondrial cytochrome c

    Alignment data:

    Expectation value = 1.35e-76, Score = 224 bits (569),

    Identities = 99% (107/108), Positive = 99% (107/108), Gaps = 0% (0/108).

    Interface alignment data:

    Interface residues in alignment: 100% (19/19).

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

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    1u74_B: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

    dssp: ---------HHHHHHHHH-----E-----------E------------------HHHHHH


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKA E

    1u74_B: 61 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKASE 108

    dssp: -----HHHHHHH---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: 1u74_A; Cytochrome c peroxidase, CCP

    Alignment data:

    Expectation value = 0, Score = 611 bits (1575),

    Identities = 99% (292/294), 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

    1u74_A: 3 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 62

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    1u74_A: 63 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 122

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    1u74_A: 123 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 182

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    1u74_A: 183 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 242

    dssp: -HHHH---EE----------HHHHHHHH---EEEE-----EEEE-----EE-HHHHHHHH


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    1u74_A: 243 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 296

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


    Download alignment FASTA file