Interaction between Cytochrome c iso-1 (5cie_B) and Cytochrome c peroxidase, mitochondrial (5cie_A)

PDB and SCOP data

PDB ID: 5cie (all binary interactions in this PDB entry)

Title: Complex of yeast cytochrome c peroxidase (W191G) bound to aniline with iso-1 cytochrome c

Release date: 2016-08-03

Resolution: 2.6 Å

  • Chain A: 5cie_B

    Title: Cytochrome c iso-1

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 108

  • Chain B: 5cie_A

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae S288C

    Number of residues: 294

Buried interface area: 524.62 Å2

Number of inter-residue contacts at the interface: 39

Number of H-bonds: 2

Number of salt bridges: 1

  • Pairwise interaction

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  • Biological assembly

    Heteromer, 4 proteins.

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  • Interface residues in 5cie_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 10 K 22.4 24.1 %
    2 8 13 T 12.7 26.5 %
    3 9 14 L 19.0 95.5 %
    4 12 17 T 46.2 60.2 %
    5 13 18 R 62.4 73.9 %
    6 16 21 Q 31.8 34.2 %
    7 17 22 C 9.6 100.0 %
    8 28 33 V 24.1 27.5 %
    9 70 75 N 17.6 55.2 %
    10 71 76 P <0.1 2.3 %
    11 72 77 K 57.3 40.2 %
    12 73 78 K 0.6 0.4 %
    13 81 86 A 47.6 69.4 %
    14 82 87 F 28.2 83.1 %
    15 83 88 G 33.0 54.7 %
    16 86 91 K 57.0 46.5 %
    17 87 92 K 39.5 29.9 %
    18 90 95 D 15.5 52.2 %

  • Interface residues in 5cie_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 58.6 47.1 %
    2 32 32 E 14.5 11.0 %
    3 34 34 D 39.8 62.3 %
    4 35 35 E 9.7 8.2 %
    5 38 38 N 26.8 19.9 %
    6 39 39 Y 100.0 82.1 %
    7 120 120 Q 59.5 52.4 %
    8 193 193 A 48.2 88.8 %
    9 194 194 A 14.5 72.4 %
    10 196 196 N 31.6 50.8 %
    11 197 197 V 37.0 92.3 %
    12 199 199 T 13.1 38.9 %
    13 201 201 E 1.9 7.3 %
    14 229 229 Y 15.3 38.5 %
    15 290 290 E 44.2 34.3 %
    16 294 294 L 9.8 8.5 %

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 35 E 9.7
2 5 10 K 39 39 Y 12.7
3 8 13 T 39 39 Y 12.7
4 9 14 L 39 39 Y 19.0
5 12 17 T 38 38 N 26.8
6 12 17 T 39 39 Y 19.4
7 13 18 R 34 34 D 15.6
8 13 18 R 39 39 Y 30.3
9 13 18 R 196 196 N 16.4
10 16 21 Q 193 193 A 27.8
11 16 21 Q 229 229 Y 4.0
12 17 22 C 193 193 A 9.6
13 28 33 V 193 193 A 10.8
14 28 33 V 201 201 E 1.9
15 28 33 V 229 229 Y 11.3
16 70 75 N 290 290 E 16.8
17 70 75 N 294 294 L 0.9
18 71 76 P 120 120 Q <0.1
19 72 77 K 120 120 Q 30.5
20 72 77 K 290 290 E 26.9 H-bond, Salt bridge
21 73 78 K 290 290 E 0.6
22 81 86 A 120 120 Q 1.4
23 81 86 A 194 194 A 14.5
24 81 86 A 196 196 N 0.2
25 81 86 A 197 197 V 18.2
26 81 86 A 199 199 T 13.1
27 82 87 F 120 120 Q 12.9 H-bond
28 82 87 F 196 196 N 5.5
29 82 87 F 197 197 V 9.8
30 83 88 G 120 120 Q 14.6
31 83 88 G 196 196 N 9.4
32 83 88 G 197 197 V 9.0
33 86 91 K 31 31 R 48.1
34 86 91 K 294 294 L 8.9
35 87 92 K 31 31 R 10.5
36 87 92 K 32 32 E 14.5
37 87 92 K 34 34 D 14.5
38 90 95 D 34 34 D 9.6
39 90 95 D 39 39 Y 5.9

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A5cie_B201HEM 640.721.7

  • 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: 5cie_B; Cytochrome c iso-1

    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

    5cie_B: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60

    dssp: -------HHHHHHHHHHH------------------------------------HHHHHH


    Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

    5cie_B: 61 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 108

    dssp: -----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: 5cie_A; Cytochrome c peroxidase, mitochondrial

    Alignment data:

    Expectation value = 0, Score = 607 bits (1564),

    Identities = 99% (291/294), Positive = 99% (291/294), 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

    5cie_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    5cie_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    5cie_A: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGP GAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    5cie_A: 181 HLKNSGYEGPGGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    5cie_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file