Interaction between Mitochondrial cytochrome c (1u74_D) and Cytochrome c peroxidase, CCP (1u74_C)

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_D

    Title: Mitochondrial cytochrome c

    Source organism: Saccharomyces cerevisiae

    Number of residues: 108

    SCOP family: a.3.1.1

  • Chain B: 1u74_C

    Title: Cytochrome c peroxidase, CCP

    Source organism: Saccharomyces cerevisiae

    Number of residues: 296 (1 missing in structure)

    SCOP family: a.93.1.1

Buried interface area: 558.81 Å2

Number of inter-residue contacts at the interface: 45

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, 2 domains.

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Create a structural model for this interaction

  • Interface residues in 1u74_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 10 10 K 16.5 14.7 %
    2 13 13 T 7.6 11.5 %
    3 14 14 L 23.3 99.3 %
    4 17 17 T 56.2 63.7 %
    5 18 18 R 67.7 76.5 %
    6 21 21 Q 48.5 47.4 %
    7 22 22 C 8.2 100.0 %
    8 33 33 V 24.2 30.5 %
    9 75 75 N 23.1 44.8 %
    10 77 77 K 49.2 42.3 %
    11 78 78 K 8.0 4.8 %
    12 86 86 A 52.9 72.8 %
    13 87 87 F 20.3 84.1 %
    14 88 88 G 33.7 65.6 %
    15 90 90 L 1.1 36.7 %
    16 91 91 K 40.8 32.4 %
    17 92 92 K 58.6 46.4 %
    18 95 95 D 18.8 50.2 %

  • Interface residues in 1u74_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 33 R 43.1 40.2 %
    2 32 34 E 30.3 23.4 %
    3 34 36 D 51.2 73.1 %
    4 35 37 E 7.3 6.1 %
    5 38 40 N 34.3 23.7 %
    6 39 41 Y 106.7 79.3 %
    7 40 42 I 0.3 1.7 %
    8 120 122 Q 60.3 55.4 %
    9 192 194 G 0.3 12.2 %
    10 193 195 A 44.4 97.6 %
    11 194 196 A 17.9 82.7 %
    12 195 197 N 13.3 41.6 %
    13 196 198 N 25.5 46.5 %
    14 197 199 V 39.9 92.0 %
    15 199 201 T 14.4 36.4 %
    16 201 203 E 1.4 5.6 %
    17 227 229 S 0.7 1.2 %
    18 229 231 Y 22.8 58.6 %
    19 290 292 E 43.9 31.9 %
    20 294 296 L 1.0 1.0 %

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 10 10 K 35 37 E 5.3
2 10 10 K 39 41 Y 11.2
3 13 13 T 39 41 Y 7.6
4 14 14 L 39 41 Y 23.3
5 17 17 T 38 40 N 34.3
6 17 17 T 39 41 Y 19.8
7 17 17 T 40 42 I 0.3
8 17 17 T 195 197 N 1.8
9 18 18 R 34 36 D 17.3
10 18 18 R 39 41 Y 35.7
11 18 18 R 196 198 N 14.7
12 21 21 Q 192 194 G 0.3
13 21 21 Q 193 195 A 27.3
14 21 21 Q 195 197 N 11.4
15 21 21 Q 227 229 S 0.7
16 21 21 Q 229 231 Y 8.8
17 22 22 C 193 195 A 8.2
18 33 33 V 193 195 A 8.9
19 33 33 V 201 203 E 1.4
20 33 33 V 229 231 Y 14.0
21 75 75 N 290 292 E 23.1
22 77 77 K 120 122 Q 36.4
23 77 77 K 290 292 E 12.8
24 78 78 K 290 292 E 8.0
25 86 86 A 120 122 Q 0.5
26 86 86 A 194 196 A 17.9
27 86 86 A 196 198 N 0.6
28 86 86 A 197 199 V 19.6
29 86 86 A 199 201 T 14.4
30 87 87 F 120 122 Q 6.8
31 87 87 F 196 198 N 4.9
32 87 87 F 197 199 V 8.5
33 88 88 G 120 122 Q 16.6
34 88 88 G 196 198 N 5.3
35 88 88 G 197 199 V 11.8
36 90 90 L 34 36 D 1.1
37 91 91 K 31 33 R 36.1
38 91 91 K 34 36 D 3.8
39 91 91 K 294 296 L 1.0
40 92 92 K 31 33 R 7.0
41 92 92 K 32 34 E 30.3 H-bond
42 92 92 K 34 36 D 19.3 H-bond, Salt bridge
43 92 92 K 35 37 E 2.1
44 95 95 D 34 36 D 9.8
45 95 95 D 39 41 Y 9.0

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A1u74_D1301HEM 630.224.1

  • 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: 1u74_D; 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% (18/18).

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

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    1u74_D: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

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


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKA E

    1u74_D: 61 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKASE 108

    dssp: --E----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_C; 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% (20/20).

    Identities = 100% (20/20), Positive = 100% (20/20), Gaps = 0% (0/20).

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    1u74_C: 3 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 62

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    1u74_C: 63 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 122

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    1u74_C: 123 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 182

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    1u74_C: 183 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 242

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    1u74_C: 243 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 296

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


    Download alignment FASTA file