Interaction between Mitochondrial cytochrome c (2pcc_B) and Cytochrome c peroxidase, CCP (2pcc_A)

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_B

    Title: Mitochondrial cytochrome c

    Source organism: Saccharomyces cerevisiae

    Number of residues: 108

    SCOP family: a.3.1.1

  • Chain B: 2pcc_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: 525.86 Å2

Number of inter-residue contacts at the interface: 42

Number of H-bonds: 1

Number of salt bridges: 2

  • Pairwise interaction

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  • Biological assembly

    Heteromer, 2 proteins, 2 domains.

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Create a structural model for this interaction

  • Interface residues in 2pcc_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 10 K 17.2 20.1 %
    2 8 13 T 7.4 11.9 %
    3 9 14 L 21.1 95.3 %
    4 11 16 K 3.7 3.6 %
    5 12 17 T 50.8 65.3 %
    6 13 18 R 65.2 72.5 %
    7 16 21 Q 45.7 45.9 %
    8 17 22 C 6.7 100.0 %
    9 28 33 V 22.0 26.7 %
    10 70 75 N 15.4 33.6 %
    11 72 77 K 33.0 29.8 %
    12 73 78 K 31.2 18.9 %
    13 81 86 A 47.7 76.5 %
    14 82 87 F 20.5 73.4 %
    15 83 88 G 26.2 45.6 %
    16 86 91 K 48.3 38.3 %
    17 87 92 K 52.5 41.0 %
    18 90 95 D 11.3 47.5 %

  • Interface residues in 2pcc_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 33 R 52.9 48.5 %
    2 32 34 E 26.6 23.9 %
    3 34 36 D 44.6 62.4 %
    4 35 37 E 8.3 7.1 %
    5 38 40 N 35.2 26.0 %
    6 39 41 Y 94.3 77.6 %
    7 120 122 Q 40.7 36.1 %
    8 193 195 A 45.8 96.3 %
    9 194 196 A 17.7 77.5 %
    10 195 197 N 11.5 36.0 %
    11 196 198 N 25.7 44.6 %
    12 197 199 V 39.4 95.1 %
    13 199 201 T 19.5 51.3 %
    14 201 203 E 0.1 0.5 %
    15 229 231 Y 16.9 42.0 %
    16 290 292 E 46.6 34.5 %

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 5 10 K 35 37 E 7.1
2 5 10 K 39 41 Y 10.1
3 8 13 T 39 41 Y 7.4
4 9 14 L 39 41 Y 21.1
5 11 16 K 38 40 N 3.7
6 12 17 T 38 40 N 31.5
7 12 17 T 39 41 Y 19.3
8 13 18 R 34 36 D 16.1
9 13 18 R 39 41 Y 33.6
10 13 18 R 196 198 N 15.6
11 16 21 Q 193 195 A 28.8
12 16 21 Q 194 196 A 0.2
13 16 21 Q 195 197 N 11.5
14 16 21 Q 229 231 Y 5.3
15 17 22 C 193 195 A 6.7
16 28 33 V 193 195 A 10.3
17 28 33 V 201 203 E 0.1
18 28 33 V 229 231 Y 11.6
19 70 75 N 290 292 E 15.4
20 72 77 K 120 122 Q 21.4
21 72 77 K 197 199 V 4.3
22 72 77 K 199 201 T 7.3
23 73 78 K 290 292 E 31.2 Salt bridge
24 81 86 A 194 196 A 17.5
25 81 86 A 196 198 N 0.3
26 81 86 A 197 199 V 17.6
27 81 86 A 199 201 T 12.2
28 82 87 F 120 122 Q 7.6
29 82 87 F 196 198 N 4.1
30 82 87 F 197 199 V 8.8
31 83 88 G 120 122 Q 11.8
32 83 88 G 196 198 N 5.7
33 83 88 G 197 199 V 8.7
34 86 91 K 31 33 R 45.8
35 86 91 K 34 36 D 2.5
36 87 92 K 31 33 R 7.1
37 87 92 K 32 34 E 26.6 H-bond
38 87 92 K 34 36 D 18.9 Salt bridge
39 87 92 K 35 37 E <0.1
40 90 95 D 34 36 D 7.2
41 90 95 D 35 37 E 1.2
42 90 95 D 39 41 Y 2.9

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A2pcc_B104HEM 629.122.9

  • 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_B; 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% (18/18).

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

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    2pcc_B: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

    dssp: ---------HHHHHHHHHH------------------------E----------HHHH--


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    2pcc_B: 61 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 108

    dssp: --E--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: 2pcc_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

    2pcc_A: 3 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 62

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    2pcc_A: 63 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 122

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    2pcc_A: 123 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 182

    dssp: -----E--------HHH-------------HHHHHHHHHHH---HHHHHHHHHHHH--EE


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    2pcc_A: 183 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 242

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    2pcc_A: 243 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 296

    dssp: ----HHHHHHHHH-HHHHHHHHHHHHHHHHH---E--------E-----HHH--


    Download alignment FASTA file