Interaction between Mitochondrial cytochrome c (2pcc_D) and Cytochrome c peroxidase, CCP (2pcc_C)

PDB and SCOP data

PDB ID: 2pcc (all binary interactions in this PDB entry)

Title: CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ELECTRON TRANSFER PARTNERS, CYTOCHROME C PEROXIDASE AND CYTOCHROME C

Release date: 1993-07-15

Resolution: 2.3 Å

  • Chain A: 2pcc_D

    Title: Mitochondrial cytochrome c

    Source organism: Saccharomyces cerevisiae

    Number of residues: 108

    SCOP family: a.3.1.1

  • Chain B: 2pcc_C

    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: 498.34 Å2

Number of inter-residue contacts at the interface: 40

Number of H-bonds: 3

Number of salt bridges: 1

  • Pairwise interaction

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  • Biological assembly

    Heteromer, 2 proteins, 2 domains.

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  • Interface residues in 2pcc_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 10 K 13.9 18.7 %
    2 8 13 T 9.4 13.3 %
    3 9 14 L 22.1 90.0 %
    4 12 17 T 51.7 55.8 %
    5 13 18 R 56.4 68.5 %
    6 16 21 Q 38.3 42.4 %
    7 17 22 C 6.6 100.0 %
    8 28 33 V 25.5 27.5 %
    9 70 75 N 20.6 45.2 %
    10 72 77 K 26.3 24.2 %
    11 73 78 K 16.3 10.0 %
    12 81 86 A 43.0 79.9 %
    13 82 87 F 21.3 75.0 %
    14 83 88 G 35.4 55.6 %
    15 86 91 K 49.2 40.4 %
    16 87 92 K 51.8 39.4 %
    17 90 95 D 10.7 46.0 %

  • Interface residues in 2pcc_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 33 R 49.2 43.0 %
    2 32 34 E 27.6 25.4 %
    3 34 36 D 41.6 63.1 %
    4 35 37 E 3.0 2.5 %
    5 38 40 N 30.7 22.4 %
    6 39 41 Y 98.4 72.0 %
    7 120 122 Q 42.6 36.6 %
    8 193 195 A 46.2 95.7 %
    9 194 196 A 12.5 70.3 %
    10 195 197 N 8.2 34.4 %
    11 196 198 N 19.9 35.8 %
    12 197 199 V 41.5 93.4 %
    13 199 201 T 17.2 47.9 %
    14 201 203 E 0.2 0.8 %
    15 229 231 Y 14.9 39.4 %
    16 290 292 E 44.7 32.3 %

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 10 K 35 37 E 2.9
2 5 10 K 39 41 Y 11.0
3 8 13 T 39 41 Y 9.4
4 9 14 L 39 41 Y 22.1
5 12 17 T 38 40 N 30.7
6 12 17 T 39 41 Y 21.0
7 13 18 R 34 36 D 17.2 Salt bridge
8 13 18 R 39 41 Y 32.4
9 13 18 R 196 198 N 6.8
10 16 21 Q 193 195 A 27.5 H-bond
11 16 21 Q 194 196 A 0.9
12 16 21 Q 195 197 N 8.2
13 16 21 Q 229 231 Y 1.7
14 17 22 C 193 195 A 6.6
15 28 33 V 193 195 A 12.1
16 28 33 V 201 203 E 0.2
17 28 33 V 229 231 Y 13.2
18 70 75 N 290 292 E 20.6 H-bond
19 72 77 K 120 122 Q 17.2
20 72 77 K 197 199 V 6.0
21 72 77 K 199 201 T 3.2
22 73 78 K 290 292 E 16.3
23 81 86 A 120 122 Q 0.2
24 81 86 A 194 196 A 11.6
25 81 86 A 197 199 V 17.1
26 81 86 A 199 201 T 14.1
27 82 87 F 120 122 Q 9.6
28 82 87 F 196 198 N 1.2
29 82 87 F 197 199 V 10.5
30 83 88 G 120 122 Q 15.6
31 83 88 G 196 198 N 11.9
32 83 88 G 197 199 V 7.9
33 86 91 K 31 33 R 41.4
34 86 91 K 290 292 E 7.8
35 87 92 K 31 33 R 7.8
36 87 92 K 32 34 E 27.6 H-bond
37 87 92 K 34 36 D 16.3
38 87 92 K 35 37 E <0.1
39 90 95 D 34 36 D 8.2
40 90 95 D 39 41 Y 2.5

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A2pcc_D104HEM 631.024.8

  • 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: 2pcc_D; Mitochondrial cytochrome c

    Alignment data:

    Expectation value = 1.54e-77, Score = 226 bits (575),

    Identities = 100% (108/108), Positive = 100% (108/108), Gaps = 0% (0/108).

    Interface alignment data:

    Interface residues in alignment: 100% (17/17).

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

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    2pcc_D: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

    dssp: ---------HHHHHHHHH-------------------------E----------HHHHH-


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    2pcc_D: 61 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 108

    dssp: --E----HHHHH---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: 2pcc_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% (16/16).

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

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    2pcc_C: 3 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 62

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    2pcc_C: 63 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 122

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    2pcc_C: 123 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 182

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    2pcc_C: 183 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 242

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    2pcc_C: 243 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 296

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


    Download alignment FASTA file