Interaction between Cytochrome c (4nfg_B) and Cytochrome c peroxidase, mitochondrial (4nfg_A)

PDB and SCOP data

PDB ID: 4nfg (all binary interactions in this PDB entry)

Title: K13R mutant of horse cytochrome c and yeast cytochrome c peroxidase complex

Release date: 2014-09-24

Resolution: 2.1 Å

  • Chain A: 4nfg_B

    Title: Cytochrome c

    Source organism: Equus caballus

    Number of residues: 104

    SCOP family: a.3.1.1

  • Chain B: 4nfg_A

    Title: Cytochrome c peroxidase, mitochondrial

    Source organism: Saccharomyces cerevisiae

    Number of residues: 294 (1 missing in structure)

    SCOP family: a.93.1.1

Buried interface area: 560.70 Å2

Number of inter-residue contacts at the interface: 42

Number of H-bonds: 4

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 4nfg_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 5 5 K 22.3 20.5 %
    2 8 8 K 45.5 36.4 %
    3 9 9 I 20.2 100.0 %
    4 12 12 Q 47.4 42.6 %
    5 13 13 R 61.6 76.4 %
    6 16 16 Q 47.3 47.7 %
    7 17 17 C 6.8 100.0 %
    8 28 28 T 12.2 14.3 %
    9 70 70 N 9.1 32.6 %
    10 72 72 K 40.0 30.8 %
    11 81 81 I 58.8 45.5 %
    12 82 82 F 10.0 33.7 %
    13 83 83 A 45.8 57.4 %
    14 85 85 I 1.6 99.6 %
    15 86 86 K 36.8 31.3 %
    16 87 87 K 66.0 52.6 %
    17 90 90 E 29.2 75.5 %

  • Interface residues in 4nfg_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 31 31 R 38.5 30.4 %
    2 32 32 E 30.9 22.8 %
    3 33 33 D 0.6 1.4 %
    4 34 34 D 51.9 73.8 %
    5 35 35 E 22.0 17.7 %
    6 38 38 N 56.6 43.4 %
    7 39 39 Y 117.3 91.1 %
    8 118 118 E 0.6 1.4 %
    9 119 119 M 0.6 5.4 %
    10 120 120 Q 44.0 39.2 %
    11 193 193 A 37.3 89.8 %
    12 194 194 A 22.9 79.6 %
    13 195 195 N 8.4 25.4 %
    14 196 196 N 27.5 46.6 %
    15 197 197 V 39.3 82.6 %
    16 199 199 T 17.8 53.1 %
    17 229 229 Y 21.4 54.5 %
    18 290 290 E 23.1 15.8 %

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 5 5 K 35 35 E 9.5
2 5 5 K 39 39 Y 12.8
3 8 8 K 35 35 E <0.1
4 8 8 K 38 38 N 19.5 H-bond
5 8 8 K 39 39 Y 26.0
6 9 9 I 39 39 Y 20.2
7 12 12 Q 38 38 N 37.1
8 12 12 Q 39 39 Y 9.4
9 12 12 Q 195 195 N 0.9
10 13 13 R 34 34 D 15.2 Salt bridge
11 13 13 R 39 39 Y 34.3
12 13 13 R 196 196 N 12.1
13 16 16 Q 193 193 A 26.4 H-bond
14 16 16 Q 195 195 N 7.5
15 16 16 Q 229 229 Y 13.3
16 17 17 C 193 193 A 6.8
17 28 28 T 193 193 A 4.1
18 28 28 T 229 229 Y 8.1
19 70 70 N 290 290 E 9.1
20 72 72 K 120 120 Q 26.0
21 72 72 K 290 290 E 14.0
22 81 81 I 194 194 A 22.9
23 81 81 I 197 197 V 18.1
24 81 81 I 199 199 T 17.8
25 82 82 F 196 196 N 3.4
26 82 82 F 197 197 V 6.6
27 83 83 A 118 118 E 0.6
28 83 83 A 119 119 M 0.6
29 83 83 A 120 120 Q 17.9
30 83 83 A 196 196 N 12.1
31 83 83 A 197 197 V 14.6
32 85 85 I 34 34 D 1.6
33 86 86 K 31 31 R 35.3
34 86 86 K 34 34 D 1.5
35 87 87 K 31 31 R 3.2
36 87 87 K 32 32 E 30.9 H-bond
37 87 87 K 33 33 D 0.6
38 87 87 K 34 34 D 20.2 H-bond, Salt bridge
39 87 87 K 35 35 E 11.1
40 90 90 E 34 34 D 13.4
41 90 90 E 35 35 E 1.4
42 90 90 E 39 39 Y 14.5

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A4nfg_B201HEC 633.824.4

  • 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: 4nfg_B; Cytochrome c

    Alignment data:

    Expectation value = 5.53e-43, Score = 139 bits (348),

    Identities = 62% (63/101), Positive = 75% (76/101), Gaps = 0% (0/101).

    Interface alignment data:

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

    Identities = 53% (9/17), Positive = 71% (12/17), Gaps = 0% (0/17).

    Query: 7 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWD 66

    G +KG +F RC QCHTVEKGG +K GPNL+G+FGR +GQA G++YTDAN K + W

    4nfg_B: 1 GDVEKGKKIFVQRCAQCHTVEKGGKNKTGPNLNGLFGRKTGQAPGFTYTDANKNKGITWK 60

    dssp: --HHHHHHHHHHH-------------------------E----------HHHH----E--


    Query: 67 ENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKA 107

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

    4nfg_B: 61 EETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKA 101

    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: 4nfg_A; Cytochrome c peroxidase, mitochondrial

    Alignment data:

    Expectation value = 0, Score = 606 bits (1561),

    Identities = 100% (290/291), Positive = 100% (290/291), Gaps = 0% (0/291).

    Interface alignment data:

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

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

    Query: 71 LVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKHDNT 130

    LVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKHDNT

    4nfg_A: 4 LVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKHDNT 63

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


    Query: 131 GGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPK 190

    GGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPK

    4nfg_A: 64 GGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPK 123

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


    Query: 191 IPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKTHLK 250

    IPWR GRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKTHLK

    4nfg_A: 124 IPWRAGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKTHLK 183

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


    Query: 251 NSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPK 310

    NSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPK

    4nfg_A: 184 NSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPK 243

    dssp: HH---EE----------HHHHHHHH---EEEE-----EEEE-----EE-HHHHHHHH-HH


    Query: 311 YLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361

    YLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

    4nfg_A: 244 YLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294

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


    Download alignment FASTA file