Interaction between Mitochondrial cytochrome c (2pcb_B) and Cytochrome c peroxidase, CCP (2pcb_A)

PDB and SCOP data

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

Title: CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ELECTRON TRANSFER PARTNERS, CYTOCHROME C PEROXIDASE AND CYTOCHROME C

Release date: 1993-07-15

Resolution: 2.8 Å

  • Chain A: 2pcb_B

    Title: Mitochondrial cytochrome c

    Source organism: Equus caballus

    Number of residues: 104

    SCOP family: a.3.1.1

  • Chain B: 2pcb_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: 504.26 Å2

Number of inter-residue contacts at the interface: 32

Number of H-bonds: 2

Number of salt bridges: 2

  • Pairwise interaction

    Download PDB coordinates

    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 2pcb_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 5 K 34.0 26.1 %
    2 8 8 K 53.7 38.8 %
    3 9 9 I 25.9 100.0 %
    4 12 12 Q 89.8 80.1 %
    5 13 13 K 48.5 62.3 %
    6 16 16 Q 35.2 37.4 %
    7 72 72 K 29.5 21.9 %
    8 81 81 I 3.9 2.7 %
    9 83 83 A 25.2 36.6 %
    10 85 85 I 3.7 52.1 %
    11 86 86 K 46.8 37.9 %
    12 87 87 K 58.1 47.4 %
    13 89 89 T 10.0 11.9 %
    14 90 90 E 37.1 95.7 %
    15 93 93 D 3.0 28.2 %

  • Interface residues in 2pcb_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 33 R 58.2 51.6 %
    2 32 34 E 24.6 18.5 %
    3 34 36 D 42.5 71.9 %
    4 35 37 E 43.8 37.6 %
    5 38 40 N 48.4 38.8 %
    6 39 41 Y 120.0 93.6 %
    7 40 42 I 17.5 66.7 %
    8 120 122 Q 18.9 15.4 %
    9 193 195 A 27.2 39.3 %
    10 194 196 A 17.0 42.9 %
    11 195 197 N 18.6 68.3 %
    12 196 198 N 28.0 51.2 %
    13 290 292 E 39.6 27.1 %

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 5 K 35 37 E 14.1
2 5 5 K 39 41 Y 19.9
3 8 8 K 38 40 N 34.6 H-bond
4 8 8 K 39 41 Y 19.0
5 9 9 I 39 41 Y 25.9
6 12 12 Q 38 40 N 13.8
7 12 12 Q 39 41 Y 16.2
8 12 12 Q 40 42 I 17.5
9 12 12 Q 193 195 A 5.8
10 12 12 Q 194 196 A 3.2
11 12 12 Q 195 197 N 18.6
12 12 12 Q 196 198 N 14.7
13 13 13 K 34 36 D 14.4 Salt bridge
14 13 13 K 39 41 Y 20.8
15 13 13 K 196 198 N 13.3
16 16 16 Q 193 195 A 21.4
17 16 16 Q 194 196 A 13.8
18 72 72 K 290 292 E 29.5 H-bond, Salt bridge
19 81 81 I 120 122 Q 3.9
20 83 83 A 120 122 Q 15.1
21 83 83 A 290 292 E 10.1
22 85 85 I 34 36 D 3.7
23 86 86 K 31 33 R 46.8
24 87 87 K 31 33 R 11.4
25 87 87 K 32 34 E 24.6
26 87 87 K 34 36 D 9.7
27 87 87 K 35 37 E 12.4
28 89 89 T 35 37 E 10.0
29 90 90 E 34 36 D 14.6
30 90 90 E 35 37 E 7.3
31 90 90 E 39 41 Y 15.1
32 93 93 D 39 41 Y 3.0

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: 2pcb_B; Mitochondrial cytochrome c

    Alignment data:

    Expectation value = 2.60e-44, Score = 142 bits (357),

    Identities = 63% (64/101), Positive = 75% (76/101), Gaps = 0% (0/101).

    Interface alignment data:

    Interface residues in alignment: 100% (15/15).

    Identities = 40% (6/15), Positive = 67% (10/15), Gaps = 0% (0/15).

    Query: 7 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 66

    G +KG +F +C QCHTVEKGG HK GPNLHG+FGR +GQA G++YTDAN K + W

    2pcb_B: 1 GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWK 60

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


    Query: 67 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKA 107

    E + EYL NPKKYIPGTKM F G+KK+ +R DLI YLKKA

    2pcb_B: 61 EETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKA 101

    dssp: HHHHHHH---HHHH--------------HHHHHHHHHHHHH


    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: 2pcb_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% (13/13).

    Identities = 100% (13/13), Positive = 100% (13/13), Gaps = 0% (0/13).

    Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127

    TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWH SGTWDKH

    2pcb_A: 3 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKH 62

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


    Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187

    DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ

    2pcb_A: 63 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 122

    dssp: --E------HHH-HHHHH-HHH---HHHHHHHHHHHHH-----HHHHHHHHHHHHHHH--


    Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247

    GPKIPWRCGRVDTPEDTTPDNGRLPDADKDA YVRTFFQRLNMNDREVVALMGAHALGKT

    2pcb_A: 123 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKT 182

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


    Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307

    HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ

    2pcb_A: 183 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 242

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


    Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    2pcb_A: 243 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 296

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


    Download alignment FASTA file