Interaction between Mitochondrial cytochrome c (d2b11b1) and Cytochrome c peroxidase, mitochondrial (2b11_A)

PDB and SCOP data

PDB ID: 2b11 (all binary interactions in this PDB entry)

Title: Crystal structure of the protein-protein complex between F82W cytochrome c and cytochrome c peroxidase

Release date: 2005-10-25

Resolution: 2.3 Å

  • Chain A: d2b11b1

    Title: Mitochondrial cytochrome c

    Source organism: Saccharomyces cerevisiae

    Number of residues: 108

    SCOP family: a.3.1.1

  • Chain B: 2b11_A

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae

    Number of residues: 294

    SCOP family: a.93.1.1

Buried interface area: 548.33 Å2

Number of inter-residue contacts at the interface: 42

Number of H-bonds: 2

Number of salt bridges: 2

  • 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 d2b11b1

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 308 13 T 9.9 12.8 %
    2 309 14 L 24.4 85.4 %
    3 312 17 T 55.1 65.9 %
    4 313 18 R 61.3 71.2 %
    5 316 21 Q 51.5 48.1 %
    6 317 22 C 14.3 34.2 %
    7 327 32 K 5.5 6.3 %
    8 328 33 V 28.8 26.4 %
    9 370 75 N 14.3 34.3 %
    10 372 77 K 34.5 30.3 %
    11 373 78 K 28.6 17.4 %
    12 381 86 A 53.8 59.7 %
    13 382 87 W 22.8 45.4 %
    14 383 88 G 19.5 34.3 %
    15 385 90 L 0.5 7.3 %
    16 386 91 K 53.0 42.9 %
    17 387 92 K 51.3 50.3 %
    18 390 95 D 19.2 51.4 %

  • Interface residues in 2b11_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 58.5 43.6 %
    2 32 32 E 19.1 15.0 %
    3 34 34 D 38.4 56.7 %
    4 35 35 E 0.2 0.2 %
    5 38 38 N 32.0 23.0 %
    6 39 39 Y 97.4 73.2 %
    7 120 120 Q 38.3 33.4 %
    8 193 193 A 53.0 90.1 %
    9 194 194 A 23.5 66.2 %
    10 195 195 N 19.3 52.6 %
    11 196 196 N 30.3 56.4 %
    12 197 197 V 43.7 92.6 %
    13 199 199 T 15.4 45.7 %
    14 227 227 S 9.4 14.0 %
    15 229 229 Y 20.6 56.9 %
    16 290 290 E 38.6 28.8 %
    17 294 294 L 10.6 9.8 %

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
1 308 13 T 39 39 Y 9.9
2 309 14 L 39 39 Y 24.4
3 312 17 T 38 38 N 32.0
4 312 17 T 39 39 Y 20.0
5 312 17 T 195 195 N 3.1
6 313 18 R 34 34 D 9.2
7 313 18 R 39 39 Y 32.5
8 313 18 R 196 196 N 19.6
9 316 21 Q 193 193 A 28.3 H-bond
10 316 21 Q 194 194 A <0.1
11 316 21 Q 195 195 N 16.2
12 316 21 Q 227 227 S 1.2
13 316 21 Q 229 229 Y 5.7
14 317 22 C 193 193 A 13.4
15 317 22 C 194 194 A 1.0
16 327 32 K 227 227 S 5.5
17 328 33 V 193 193 A 11.3
18 328 33 V 227 227 S 2.7
19 328 33 V 229 229 Y 14.8
20 370 75 N 290 290 E 14.3 H-bond
21 372 77 K 120 120 Q 34.5
22 373 78 K 290 290 E 24.3 Salt bridge
23 373 78 K 294 294 L 4.3
24 381 86 A 120 120 Q 0.2
25 381 86 A 194 194 A 22.5
26 381 86 A 197 197 V 15.8
27 381 86 A 199 199 T 15.4
28 382 87 W 120 120 Q 3.6
29 382 87 W 196 196 N 3.6
30 382 87 W 197 197 V 15.6
31 383 88 G 196 196 N 7.2
32 383 88 G 197 197 V 12.3
33 385 90 L 34 34 D 0.5
34 386 91 K 31 31 R 45.9
35 386 91 K 34 34 D 0.7
36 386 91 K 294 294 L 6.3
37 387 92 K 31 31 R 12.6
38 387 92 K 32 32 E 19.1
39 387 92 K 34 34 D 19.6 Salt bridge
40 390 95 D 34 34 D 8.3
41 390 95 D 35 35 E 0.2
42 390 95 D 39 39 Y 10.7

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: d2b11b1; Mitochondrial cytochrome c

    Alignment data:

    Expectation value = 9.85e-77, Score = 224 bits (569),

    Identities = 99% (107/108), Positive = 100% (108/108), Gaps = 0% (0/108).

    Interface alignment data:

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

    Identities = 94% (17/18), Positive = 100% (18/18), Gaps = 0% (0/18).

    Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61

    TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK

    d2b11b1: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

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


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMA+GGLKKEKDRNDLITYLKKACE

    d2b11b1: 61 NVLWDENNMSEYLTNPKKYIPGTKMAWGGLKKEKDRNDLITYLKKACE 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: 2b11_A; Cytochrome c peroxidase, mitochondrial

    Alignment data:

    Expectation value = 0, Score = 616 bits (1588),

    Identities = 100% (294/294), Positive = 100% (294/294), Gaps = 0% (0/294).

    Interface alignment data:

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

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

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH

    2b11_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    2b11_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT

    2b11_A: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    2b11_A: 181 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    2b11_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file