Interaction between Cytochrome c (4ged_B) and Ascorbate peroxidase (4ged_A)

PDB and SCOP data

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

Title: Crystal Structure of the Leishmania Major Peroxidase-Cytochrome C Complex

Release date: 2012-10-24

Resolution: 1.8 Å

  • Chain A: 4ged_B

    Title: Cytochrome c

    Source organism: Leishmania major

    Number of residues: 113 (11 missing in structure)

    SCOP family: a.3.1.1

  • Chain B: 4ged_A

    Title: Ascorbate peroxidase

    Source organism: Leishmania major

    Number of residues: 268

Buried interface area: 555.84 Å2

Number of inter-residue contacts at the interface: 55

Number of H-bonds: 6

Number of salt bridges: 2

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 2 proteins, 1 domain.

    Download PDB coordinates


A structural model for this interaction has been created.

Download modeled structure

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  • Interface residues in 4ged_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 19 19 K 5.9 4.9 %
    2 20 20 L 31.4 64.4 %
    3 23 23 G 39.5 67.6 %
    4 24 24 R 75.2 82.3 %
    5 27 27 Q 88.6 58.3 %
    6 28 28 C 11.6 70.5 %
    7 39 39 V 39.9 47.1 %
    8 83 83 K 7.4 7.3 %
    9 92 92 S 45.4 58.7 %
    10 93 93 F 19.1 78.6 %
    11 94 94 A 59.9 84.3 %
    12 95 95 G 10.2 99.1 %
    13 96 96 I 0.4 4.5 %
    14 97 97 K 45.7 37.1 %
    15 98 98 K 49.0 39.6 %
    16 101 101 E 26.5 52.9 %

  • Interface residues in 4ged_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 49 16 E 30.3 52.3 %
    2 53 20 S 11.3 16.6 %
    3 54 21 E 2.9 1.9 %
    4 56 23 L 49.5 73.6 %
    5 57 24 E 4.6 6.1 %
    6 133 100 E 11.1 14.6 %
    7 134 101 Y 58.9 71.0 %
    8 135 102 M 17.2 84.8 %
    9 136 103 G 39.0 76.6 %
    10 137 104 G 1.8 13.3 %
    11 207 174 P 13.3 46.2 %
    12 209 176 T 4.9 72.9 %
    13 210 177 H 72.7 86.2 %
    14 211 178 D 55.0 97.5 %
    15 212 179 K 30.8 42.9 %
    16 213 180 N 39.5 92.0 %
    17 214 181 G 13.0 100.0 %
    18 215 182 F 10.4 96.7 %
    19 216 183 D 37.2 81.4 %
    20 217 184 N 3.6 19.9 %
    21 218 185 S 17.0 87.2 %
    22 221 188 T 6.9 16.6 %
    23 222 189 Q 5.1 20.8 %
    24 244 211 T 15.8 25.7 %
    25 246 213 K 1.2 0.8 %
    26 247 214 L 2.8 53.8 %

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 19 19 K 54 21 E 2.9
2 19 19 K 56 23 L 3.0
3 20 20 L 53 20 S 5.9
4 20 20 L 56 23 L 19.8
5 20 20 L 134 101 Y 5.7
6 23 23 G 56 23 L 13.8
7 23 23 G 57 24 E 4.6
8 23 23 G 211 178 D 0.2
9 23 23 G 212 179 K 2.4
10 23 23 G 213 180 N 18.5 H-bond
11 24 24 R 56 23 L 13.0
12 24 24 R 134 101 Y 3.3
13 24 24 R 135 102 M 8.0
14 24 24 R 210 177 H 1.5
15 24 24 R 211 178 D 21.3 H-bond, Salt bridge
16 24 24 R 213 180 N 21.0
17 24 24 R 214 181 G 7.2
18 27 27 Q 207 174 P 13.3
19 27 27 Q 209 176 T 4.9
20 27 27 Q 210 177 H 35.5
21 27 27 Q 211 178 D 2.5
22 27 27 Q 212 179 K 28.4 H-bond
23 27 27 Q 246 213 K 1.2
24 27 27 Q 247 214 L 2.8
25 28 28 C 210 177 H 11.6
26 39 39 V 210 177 H 24.1
27 39 39 V 244 211 T 15.8
28 83 83 K 216 183 D 3.9
29 83 83 K 217 184 N 3.6
30 92 92 S 211 178 D 10.1
31 92 92 S 216 183 D 6.4
32 92 92 S 218 185 S 17.0
33 92 92 S 221 188 T 6.9
34 92 92 S 222 189 Q 5.1
35 93 93 F 211 178 D 12.5
36 93 93 F 216 183 D 6.6
37 94 94 A 135 102 M 5.7
38 94 94 A 136 103 G 9.2
39 94 94 A 211 178 D 8.5 H-bond
40 94 94 A 214 181 G 5.8
41 94 94 A 215 182 F 10.4
42 94 94 A 216 183 D 20.3
43 95 95 G 134 101 Y 1.8
44 95 95 G 135 102 M 3.6
45 95 95 G 136 103 G 4.8
46 96 96 I 134 101 Y 0.4
47 97 97 K 133 100 E 10.9
48 97 97 K 134 101 Y 8.1
49 97 97 K 136 103 G 25.0
50 97 97 K 137 104 G 1.8
51 98 98 K 49 16 E 30.3 H-bond, Salt bridge
52 98 98 K 133 100 E 0.2
53 98 98 K 134 101 Y 18.5
54 101 101 E 53 20 S 5.4
55 101 101 E 134 101 Y 21.1 H-bond

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A4ged_B201HEC 614.031.1
B4ged_A402K 60.20.4

  • 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: 4ged_B; Cytochrome c

    Alignment data:

    Expectation value = 4.47e-33, Score = 114 bits (283),

    Identities = 49% (50/102), Positive = 67% (68/102), Gaps = 0% (0/102).

    Interface alignment data:

    Interface residues in alignment: 100% (16/16).

    Identities = 62% (10/16), Positive = 81% (13/16), Gaps = 0% (0/16).

    Query: 4 FKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNV 63

    G ++G LFK R QCHT KGG + VGPNL GI R SG+ EG++Y+ AN + V

    4ged_B: 9 LPPGDVERGEKLFKGRAAQCHTATKGGSNGVGPNLFGIVNRPSGKVEGFTYSKANAESGV 68

    dssp: --HHHHHHHHHHH-------------------------E----------HHHHH---


    Query: 64 LWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLK 105

    +W + YL NPKK++PGTKM+F G+KK ++R D+I YL+

    4ged_B: 69 IWTPEVLDVYLENPKKFMPGTKMSFAGIKKPQERADVIAYLE 110

    dssp: E--HHHHHHHHH-HHHH-------------HHHHHHHHHHHH


    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: 4ged_A; Ascorbate peroxidase

    Alignment data:

    Expectation value = 2.92e-58, Score = 193 bits (488),

    Identities = 41% (107/263), Positive = 55% (145/263), Gaps = 2% (4/263).

    Interface alignment data:

    Interface residues in alignment: 100% (26/26).

    Identities = 23% (6/26), Positive = 35% (9/26), Gaps = 0% (0/26).

    Query: 90 YNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKHDNTGGSYGGTYRFKKEFNDPSN 149

    ++ AL+ +D + GP L+RLAWH + ++D G + RFK E N

    4ged_A: 6 FDIRALRADIEDMISEKLELGPSLIRLAWHEAASYDCFKKDGSPNSASMRFKPECLYAGN 65

    dssp: --HHHHHHHHHHHHHH---HHHHHHHHHHHHH---E----E------HHH---HHH-HHH


    Query: 150 AGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTT--PD 207

    GL K LE + K++P IS DL+ L A++ M GP IP+ GRVD + + PD

    4ged_A: 66 KGLDIPRKALETLKKKYPQISYADLWVLAAYVAIEYMGGPTIPFCWGRVDAKDGSVCGPD 125

    dssp: ---HHHHHHHHHHHHH-----HHHHHHHHHHHHHHH--------EE-------HHH----


    Query: 208 NGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTN 267

    GRLPD K +VR F+RL ND+E VAL+GAH G+ H++ SGY GPW N F N

    4ged_A: 126 -GRLPDGSKTQSHVREVFRRLGFNDQETVALIGAHTCGECHIEFSGYHGPWTHDKNGFDN 184

    dssp: ---------HHHHHHHHHHH---HHHHHHHHHHHH--EE-HHHH---EE----------


    Query: 268 EFYLNLLNEDWKLEKNDANNEQWD-SKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFF 326

    F+ LL+EDW L + D + + MMLP+D L+ DP Y V+ YA D D+F

    4ged_A: 185 SFFTQLLDEDWVLNPKVEQMQLMDRATTKLMMLPSDVCLLLDPSYRKYVELYAKDNDRFN 244

    dssp: HHHHHHHH--EEE--------EEE------EE-HHHHHHHH-HHHHHHHHHHHH-HHHHH


    Query: 327 KDFSKAFEKLLENGITFPKDAPS 349

    KDF+ AF+KL E G AP+

    4ged_A: 245 KDFANAFKKLTELGTRNLHKAPA 267

    dssp: HHHHHHHHHH--------EE---


    Download alignment FASTA file