Interaction between Mitochondrial cytochrome c (2bcn_B) and Cytochrome c peroxidase, CCP (2bcn_A)

PDB and SCOP data

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

Title: Solvent isotope effects on interfacial protein electron transfer between cytochrome c and cytochrome c peroxidase

Release date: 2006-02-28

Resolution: 1.7 Å

  • Chain A: 2bcn_B

    Title: Mitochondrial cytochrome c

    Source organism: Saccharomyces cerevisiae

    Number of residues: 108

    SCOP family: a.3.1.1

  • Chain B: 2bcn_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: 550.66 Å2

Number of inter-residue contacts at the interface: 42

  • 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 2bcn_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 10 10 K 25.7 26.5 %
    2 13 13 T 15.1 20.8 %
    3 14 14 L 21.1 94.8 %
    4 17 17 T 55.9 70.7 %
    5 18 18 R 67.1 77.6 %
    6 21 21 Q 48.9 51.8 %
    7 22 22 C 7.8 100.0 %
    8 33 33 V 25.6 30.3 %
    9 75 75 N 24.7 42.1 %
    10 77 77 K 10.9 9.4 %
    11 78 78 K 3.2 2.1 %
    12 86 86 A 47.2 67.7 %
    13 87 87 F 26.1 80.4 %
    14 88 88 G 33.1 57.4 %
    15 90 90 L 0.2 10.4 %
    16 91 91 K 59.5 53.2 %
    17 92 92 K 60.2 52.7 %
    18 95 95 D 18.4 62.6 %

  • Interface residues in 2bcn_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 33 R 70.7 52.7 %
    2 32 34 E 24.4 21.3 %
    3 34 36 D 48.9 71.7 %
    4 35 37 E 7.5 6.2 %
    5 38 40 N 33.7 23.6 %
    6 39 41 Y 111.8 85.4 %
    7 40 42 I 1.0 6.5 %
    8 120 122 Q 35.6 30.1 %
    9 193 195 A 42.7 97.7 %
    10 194 196 A 16.8 84.8 %
    11 195 197 N 18.9 50.7 %
    12 196 198 N 30.2 54.2 %
    13 197 199 V 36.1 89.0 %
    14 199 201 T 14.6 40.6 %
    15 201 203 E 2.5 10.8 %
    16 227 229 S <0.1 0.1 %
    17 229 231 Y 22.8 63.9 %
    18 290 292 E 27.7 20.0 %
    19 294 296 L 4.6 4.5 %

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 10 10 K 35 37 E 7.5
2 10 10 K 39 41 Y 18.1
3 13 13 T 39 41 Y 15.1
4 14 14 L 39 41 Y 21.1
5 17 17 T 38 40 N 33.7
6 17 17 T 39 41 Y 16.5
7 17 17 T 40 42 I 1.0
8 17 17 T 195 197 N 4.7
9 18 18 R 34 36 D 17.7
10 18 18 R 39 41 Y 33.4
11 18 18 R 196 198 N 16.0
12 21 21 Q 193 195 A 27.1
13 21 21 Q 195 197 N 14.2
14 21 21 Q 227 229 S <0.1
15 21 21 Q 229 231 Y 7.5
16 22 22 C 193 195 A 7.8
17 33 33 V 193 195 A 7.8
18 33 33 V 201 203 E 2.5
19 33 33 V 229 231 Y 15.3
20 75 75 N 290 292 E 24.4
21 75 75 N 294 296 L 0.3
22 77 77 K 120 122 Q 10.9
23 78 78 K 290 292 E 3.2
24 86 86 A 194 196 A 16.8
25 86 86 A 197 199 V 15.8
26 86 86 A 199 201 T 14.6
27 87 87 F 120 122 Q 11.1
28 87 87 F 196 198 N 3.6
29 87 87 F 197 199 V 11.3
30 88 88 G 120 122 Q 13.6
31 88 88 G 196 198 N 10.6
32 88 88 G 197 199 V 9.0
33 90 90 L 34 36 D 0.2
34 91 91 K 31 33 R 52.2
35 91 91 K 34 36 D 2.8
36 91 91 K 290 292 E 0.1
37 91 91 K 294 296 L 4.4
38 92 92 K 31 33 R 18.5
39 92 92 K 32 34 E 24.4
40 92 92 K 34 36 D 17.3
41 95 95 D 34 36 D 10.9
42 95 95 D 39 41 Y 7.5

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A2bcn_B109HEM 644.823.6

  • 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: 2bcn_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% (18/18).

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

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    2bcn_B: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

    dssp: ---------HHHHHHHHH-----E-----------E-------E----------HHHH--


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKA E

    2bcn_B: 61 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKASE 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: 2bcn_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% (19/19).

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

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    2bcn_A: 3 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 62

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    2bcn_A: 63 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 122

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    2bcn_A: 123 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 182

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    2bcn_A: 183 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 242

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    2bcn_A: 243 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 296

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


    Download alignment FASTA file