Interaction between Mitochondrial cytochrome c (1s6v_B) and Cytochrome c peroxidase, CCP (1s6v_A)

PDB and SCOP data

PDB ID: 1s6v (all binary interactions in this PDB entry)

Title: Structure of a cytochrome c peroxidase-cytochrome c site specific cross-link

Release date: 2004-04-27

Resolution: 1.9 Å

  • Chain A: 1s6v_B

    Title: Mitochondrial cytochrome c

    Source organism: Saccharomyces cerevisiae

    Number of residues: 108

    SCOP family: a.3.1.1

  • Chain B: 1s6v_A

    Title: Cytochrome c peroxidase, CCP

    Source organism: Saccharomyces cerevisiae

    Number of residues: 294

    SCOP family: a.93.1.1

Buried interface area: 266.26 Å2

Number of inter-residue contacts at the interface: 25

Number of disulphide bonds: 1

  • 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 1s6v_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 12 17 T 30.3 37.9 %
    2 13 18 R 57.9 67.2 %
    3 16 21 Q 12.7 12.6 %
    4 17 22 C 4.3 69.6 %
    5 28 33 V 38.2 44.5 %
    6 72 77 K 31.1 32.3 %
    7 73 78 K 11.5 7.3 %
    8 79 84 K 3.3 3.2 %
    9 81 86 C 61.5 91.1 %
    10 82 87 F 7.8 37.9 %
    11 83 88 G 2.3 3.9 %
    12 86 91 K 5.5 4.4 %

  • Interface residues in 1s6v_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 5.5 4.7 %
    2 34 34 D 14.4 21.6 %
    3 38 38 N 10.9 7.9 %
    4 39 39 Y 73.6 60.0 %
    5 120 120 Q 25.1 22.2 %
    6 193 193 A 27.4 61.5 %
    7 194 194 A 24.4 63.6 %
    8 195 195 N 0.9 3.2 %
    9 196 196 N 21.1 32.5 %
    10 197 197 C 36.4 85.6 %
    11 227 227 S 0.2 0.6 %
    12 229 229 Y 14.8 35.6 %
    13 290 290 E 11.5 8.3 %

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 12 17 T 38 38 N 2.6
2 12 17 T 39 39 Y 27.7
3 13 18 R 34 34 D 14.4
4 13 18 R 39 39 Y 41.5
5 13 18 R 196 196 N 1.9
6 16 21 Q 38 38 N 8.3
7 16 21 Q 39 39 Y 4.4
8 17 22 C 193 193 A 4.3
9 28 33 V 193 193 A 23.1
10 28 33 V 227 227 S 0.2
11 28 33 V 229 229 Y 14.8
12 72 77 K 120 120 Q 24.1
13 72 77 K 197 197 C 7.0
14 73 78 K 290 290 E 11.5
15 79 84 K 194 194 A 3.3
16 81 86 C 194 194 A 21.1
17 81 86 C 195 195 N 0.9
18 81 86 C 196 196 N 15.9
19 81 86 C 197 197 C 23.6 Disulphide bond
20 82 87 F 196 196 N 2.8
21 82 87 F 197 197 C 4.9
22 83 88 G 120 120 Q 1.0
23 83 88 G 196 196 N 0.5
24 83 88 G 197 197 C 0.8
25 86 91 K 31 31 R 5.5

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A1s6v_B104HEM 632.317.9

  • 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: 1s6v_B; Mitochondrial cytochrome c

    Alignment data:

    Expectation value = 1.21e-74, Score = 219 bits (556),

    Identities = 98% (105/107), Positive = 98% (105/107), Gaps = 0% (0/107).

    Interface alignment data:

    Interface residues in alignment: 100% (12/12).

    Identities = 92% (11/12), Positive = 92% (11/12), Gaps = 0% (0/12).

    Query: 3 EFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKN 62

    EFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKN

    1s6v_B: 2 EFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKN 61

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


    Query: 63 VLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    VLWDENNMSEYLTNPKKYIPGTKM FGGLKKEKDRNDLITYLKKA E

    1s6v_B: 62 VLWDENNMSEYLTNPKKYIPGTKMCFGGLKKEKDRNDLITYLKKATE 108

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


    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: 1s6v_A; Cytochrome c peroxidase, CCP

    Alignment data:

    Expectation value = 0, Score = 611 bits (1573),

    Identities = 99% (292/294), Positive = 99% (292/294), Gaps = 0% (0/294).

    Interface alignment data:

    Interface residues in alignment: 100% (13/13).

    Identities = 92% (12/13), Positive = 92% (12/13), Gaps = 0% (0/13).

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH

    1s6v_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    1s6v_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWR GRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT

    1s6v_A: 121 GPKIPWRAGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGPWGAANN FTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    1s6v_A: 181 HLKNSGYEGPWGAANNCFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    1s6v_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

    dssp: -HHHHHHHHHHH--HHHHHHHHHHHHHHHHH---E--------E-----HHH--


    Download alignment FASTA file