Interaction between Mitochondrial cytochrome c (1s6v_D) and Cytochrome c peroxidase, CCP (1s6v_C)

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_D

    Title: Mitochondrial cytochrome c

    Source organism: Saccharomyces cerevisiae

    Number of residues: 108

    SCOP family: a.3.1.1

  • Chain B: 1s6v_C

    Title: Cytochrome c peroxidase, CCP

    Source organism: Saccharomyces cerevisiae

    Number of residues: 294

    SCOP family: a.93.1.1

Buried interface area: 255.83 Å2

Number of inter-residue contacts at the interface: 24

Number of salt bridges: 1

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_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 12 17 T 30.5 40.8 %
    2 13 18 R 58.7 66.9 %
    3 16 21 Q 13.5 13.6 %
    4 17 22 C 4.5 59.4 %
    5 28 33 V 39.4 45.8 %
    6 70 75 N 3.7 9.4 %
    7 72 77 K 30.6 30.4 %
    8 73 78 K 1.8 1.1 %
    9 79 84 K 3.0 2.8 %
    10 81 86 C 62.6 90.3 %
    11 82 87 F 6.6 32.0 %
    12 83 88 G 0.2 0.4 %
    13 86 91 K 0.8 0.6 %

  • Interface residues in 1s6v_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 0.8 0.7 %
    2 34 34 D 16.1 26.0 %
    3 38 38 N 11.8 8.2 %
    4 39 39 Y 74.7 57.4 %
    5 120 120 Q 22.3 19.4 %
    6 193 193 A 27.3 59.4 %
    7 194 194 A 23.7 63.4 %
    8 195 195 N 1.0 3.8 %
    9 196 196 N 18.8 30.2 %
    10 197 197 C 37.2 80.6 %
    11 227 227 S 2.5 4.1 %
    12 229 229 Y 14.1 38.6 %
    13 290 290 E 5.5 4.0 %

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 2.9
2 12 17 T 39 39 Y 27.6
3 13 18 R 34 34 D 16.1 Salt bridge
4 13 18 R 39 39 Y 42.5
5 13 18 R 196 196 N 0.1
6 16 21 Q 38 38 N 8.9
7 16 21 Q 39 39 Y 4.6
8 17 22 C 193 193 A 4.5
9 28 33 V 193 193 A 22.8
10 28 33 V 227 227 S 2.5
11 28 33 V 229 229 Y 14.1
12 70 75 N 290 290 E 3.7
13 72 77 K 120 120 Q 22.3
14 72 77 K 197 197 C 8.3
15 73 78 K 290 290 E 1.8
16 79 84 K 194 194 A 3.0
17 81 86 C 194 194 A 20.8
18 81 86 C 195 195 N 1.0
19 81 86 C 196 196 N 16.2
20 81 86 C 197 197 C 24.6 Disulphide bond
21 82 87 F 196 196 N 2.3
22 82 87 F 197 197 C 4.3
23 83 88 G 196 196 N 0.2
24 86 91 K 31 31 R 0.8

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A1s6v_D104HEM 630.918.1

  • 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_D; 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% (13/13).

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

    Query: 3 EFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKN 62

    EFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKN

    1s6v_D: 2 EFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKN 61

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


    Query: 63 VLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109

    VLWDENNMSEYLTNPKKYIPGTKM FGGLKKEKDRNDLITYLKKA E

    1s6v_D: 62 VLWDENNMSEYLTNPKKYIPGTKMCFGGLKKEKDRNDLITYLKKATE 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: 1s6v_C; 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_C: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 60

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    1s6v_C: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120

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


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWR GRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT

    1s6v_C: 121 GPKIPWRAGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 180

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGPWGAANN FTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    1s6v_C: 181 HLKNSGYEGPWGAANNCFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240

    dssp: -HHHH---EE----------HHHHHHHH---EEEE-----EEEE-----EE-HHHHHHHH


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    1s6v_C: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file