Interaction between Mitochondrial cytochrome c (1u75_B) and Cytochrome c peroxidase, CCP (1u75_A)

PDB and SCOP data

PDB ID: 1u75 (all binary interactions in this PDB entry)

Title: Electron Transfer Complex between Horse Heart Cytochrome c and Zinc-Porphyrin Substituted Cytochrome c Peroxidase

Release date: 2004-09-28

Resolution: 2.5 Å

  • Chain A: 1u75_B

    Title: Mitochondrial cytochrome c

    Source organism: Equus caballus

    Number of residues: 104

    SCOP family: a.3.1.1

  • Chain B: 1u75_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: 543.72 Å2

Number of inter-residue contacts at the interface: 42

Number of H-bonds: 3

Number of salt bridges: 3

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 3 proteins, 3 domains.

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Create a structural model for this interaction

  • Interface residues in 1u75_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 5 K 41.3 32.4 %
    2 8 8 K 56.8 46.6 %
    3 9 9 I 25.5 100.0 %
    4 11 11 V 0.8 1.0 %
    5 12 12 Q 84.0 82.1 %
    6 13 13 K 57.3 67.8 %
    7 16 16 Q 41.3 42.5 %
    8 69 69 E 0.5 0.7 %
    9 70 70 N 0.1 0.4 %
    10 72 72 K 29.2 23.4 %
    11 82 82 F <0.1 0.2 %
    12 83 83 A 31.8 50.3 %
    13 85 85 I 2.5 40.4 %
    14 86 86 K 52.2 49.7 %
    15 87 87 K 69.8 54.7 %
    16 89 89 T 6.7 8.1 %
    17 90 90 E 38.0 88.5 %
    18 93 93 D 5.8 29.5 %

  • Interface residues in 1u75_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 33 R 58.6 51.4 %
    2 32 34 E 33.1 24.9 %
    3 33 35 D 0.9 1.9 %
    4 34 36 D 46.7 78.5 %
    5 35 37 E 40.5 34.7 %
    6 38 40 N 51.5 39.5 %
    7 39 41 Y 127.0 96.9 %
    8 40 42 I 19.1 62.9 %
    9 120 122 Q 22.0 18.5 %
    10 193 195 A 29.9 45.5 %
    11 194 196 A 18.2 46.7 %
    12 195 197 N 16.8 74.5 %
    13 196 198 N 36.5 63.5 %
    14 197 199 V 0.2 0.4 %
    15 290 292 E 40.2 28.9 %
    16 294 296 L 2.4 2.3 %

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 35 37 E 17.9
2 5 5 K 39 41 Y 23.4
3 8 8 K 38 40 N 39.6 H-bond
4 8 8 K 39 41 Y 17.2
5 9 9 I 39 41 Y 25.5
6 11 11 V 193 195 A 0.8
7 12 12 Q 38 40 N 11.9
8 12 12 Q 39 41 Y 13.2
9 12 12 Q 40 42 I 18.6
10 12 12 Q 193 195 A 5.8
11 12 12 Q 194 196 A 1.9
12 12 12 Q 195 197 N 16.8
13 12 12 Q 196 198 N 15.7 H-bond
14 13 13 K 34 36 D 17.6 Salt bridge
15 13 13 K 39 41 Y 20.0
16 13 13 K 40 42 I 0.5
17 13 13 K 196 198 N 19.3
18 16 16 Q 193 195 A 23.3
19 16 16 Q 194 196 A 16.3
20 16 16 Q 196 198 N 1.5
21 16 16 Q 197 199 V 0.1
22 69 69 E 31 33 R 0.5
23 70 70 N 290 292 E 0.1
24 72 72 K 120 122 Q <0.1
25 72 72 K 290 292 E 29.2 H-bond, Salt bridge
26 82 82 F 197 199 V <0.1
27 83 83 A 120 122 Q 22.0
28 83 83 A 290 292 E 9.8
29 85 85 I 34 36 D 2.5
30 86 86 K 31 33 R 48.5
31 86 86 K 34 36 D 0.2
32 86 86 K 290 292 E 1.1
33 86 86 K 294 296 L 2.4
34 87 87 K 31 33 R 9.6
35 87 87 K 32 34 E 33.1
36 87 87 K 33 35 D 0.9
37 87 87 K 34 36 D 10.1
38 87 87 K 35 37 E 16.0 Salt bridge
39 89 89 T 35 37 E 6.7
40 90 90 E 34 36 D 16.3
41 90 90 E 39 41 Y 21.7
42 93 93 D 39 41 Y 5.8

Analyse interface in VoroContacts server

  • 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: 1u75_B; Mitochondrial cytochrome c

    Alignment data:

    Expectation value = 2.60e-44, Score = 142 bits (357),

    Identities = 63% (64/101), Positive = 75% (76/101), Gaps = 0% (0/101).

    Interface alignment data:

    Interface residues in alignment: 100% (18/18).

    Identities = 44% (8/18), Positive = 67% (12/18), Gaps = 0% (0/18).

    Query: 7 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 66

    G +KG +F +C QCHTVEKGG HK GPNLHG+FGR +GQA G++YTDAN K + W

    1u75_B: 1 GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWK 60

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


    Query: 67 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKA 107

    E + EYL NPKKYIPGTKM F G+KK+ +R DLI YLKKA

    1u75_B: 61 EETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKA 101

    dssp: ---------------------------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: 1u75_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% (16/16).

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

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    1u75_A: 3 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 62

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    1u75_A: 63 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 122

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    1u75_A: 123 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 182

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    1u75_A: 183 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 242

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    1u75_A: 243 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 296

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


    Download alignment FASTA file