Interaction between Mitochondrial cytochrome c (d2b0zb1) and Cytochrome c peroxidase, mitochondrial (2b0z_A)
PDB and SCOP data
PDB ID: 2b0z (all binary interactions in this PDB entry)
Title: Crystal structure of the protein-protein complex between F82I cytochrome c and cytochrome c peroxidase
Release date: 2005-10-25
Resolution: 2.7 Å
Structural properties
Hetero-dimer interface properties
Buried interface area: 406.26 Å2
Number of inter-residue contacts at the interface: 44
Experimental structure
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Pairwise interaction
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Biological assembly
Heteromer, 2 proteins, 2 domains.
Interface structure modeling
Residues at the interaction interface
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Interface residues in d2b0zb1
No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, % 1 13 18 R 9.3 8.2 % 2 49 54 T 6.2 15.8 % 3 50 55 D 9.9 9.1 % 4 51 56 A 3.4 25.8 % 5 54 59 K 23.6 14.4 % 6 70 75 N 23.5 40.0 % 7 72 77 K 84.9 96.0 % 8 73 78 K 29.5 17.1 % 9 76 81 P 54.5 66.5 % 10 77 82 G 48.9 97.9 % 11 78 83 T 6.9 53.2 % 12 79 84 K 29.0 27.2 % 13 81 86 A 35.1 39.6 % 14 82 87 I 10.3 17.2 % 15 83 88 G 31.3 57.9 %
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Interface residues in 2b0z_A
No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, % 1 120 120 Q 23.9 19.3 % 2 193 193 A 48.2 84.0 % 3 194 194 A 30.7 91.0 % 4 195 195 N 1.2 3.9 % 5 197 197 V 25.2 51.0 % 6 199 199 T 29.4 80.0 % 7 200 200 N 11.2 69.1 % 8 201 201 E 34.4 95.1 % 9 204 204 L 48.1 79.1 % 10 205 205 N 12.3 99.9 % 11 208 208 N 33.2 31.1 % 12 209 209 E 20.8 44.7 % 13 226 226 K 9.9 5.1 % 14 227 227 S 28.0 47.5 % 15 229 229 Y 29.4 74.1 % 16 255 255 Q 14.3 22.9 % 17 256 256 D 6.2 5.9 %
Inter-residue contacts at the interaction interface
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 | 13 | 18 | R | 226 | 226 | K | 9.3 | |
2 | 49 | 54 | T | 200 | 200 | N | 1.7 | |
3 | 49 | 54 | T | 204 | 204 | L | 0.3 | |
4 | 49 | 54 | T | 255 | 255 | Q | 4.1 | |
5 | 50 | 55 | D | 255 | 255 | Q | 3.7 | |
6 | 50 | 55 | D | 256 | 256 | D | 6.2 | |
7 | 51 | 56 | A | 199 | 199 | T | 0.5 | |
8 | 51 | 56 | A | 255 | 255 | Q | 3.0 | |
9 | 54 | 59 | K | 120 | 120 | Q | 23.6 | |
10 | 70 | 75 | N | 193 | 193 | A | 16.5 | |
11 | 70 | 75 | N | 229 | 229 | Y | 7.0 | |
12 | 72 | 77 | K | 193 | 193 | A | 10.6 | |
13 | 72 | 77 | K | 194 | 194 | A | 8.6 | |
14 | 72 | 77 | K | 201 | 201 | E | 22.5 | |
15 | 72 | 77 | K | 204 | 204 | L | 10.1 | |
16 | 72 | 77 | K | 205 | 205 | N | 12.3 | |
17 | 72 | 77 | K | 208 | 208 | N | 0.7 | |
18 | 72 | 77 | K | 209 | 209 | E | 6.5 | |
19 | 72 | 77 | K | 229 | 229 | Y | 13.5 | |
20 | 73 | 78 | K | 193 | 193 | A | 21.0 | |
21 | 73 | 78 | K | 194 | 194 | A | 7.3 | |
22 | 73 | 78 | K | 195 | 195 | N | 1.2 | |
23 | 76 | 81 | P | 120 | 120 | Q | 0.3 | |
24 | 76 | 81 | P | 194 | 194 | A | 14.6 | |
25 | 76 | 81 | P | 197 | 197 | V | 25.2 | |
26 | 76 | 81 | P | 199 | 199 | T | 14.1 | |
27 | 76 | 81 | P | 201 | 201 | E | 0.3 | |
28 | 77 | 82 | G | 194 | 194 | A | 0.2 | |
29 | 77 | 82 | G | 199 | 199 | T | 14.8 | |
30 | 77 | 82 | G | 200 | 200 | N | 9.4 | |
31 | 77 | 82 | G | 201 | 201 | E | 11.6 | |
32 | 77 | 82 | G | 204 | 204 | L | 9.3 | |
33 | 77 | 82 | G | 255 | 255 | Q | 3.5 | |
34 | 78 | 83 | T | 204 | 204 | L | 6.9 | |
35 | 79 | 84 | K | 204 | 204 | L | 21.4 | |
36 | 79 | 84 | K | 208 | 208 | N | 7.6 | |
37 | 81 | 86 | A | 208 | 208 | N | 24.9 | |
38 | 81 | 86 | A | 209 | 209 | E | 10.2 | |
39 | 82 | 87 | I | 209 | 209 | E | 4.1 | |
40 | 82 | 87 | I | 227 | 227 | S | 1.8 | |
41 | 82 | 87 | I | 229 | 229 | Y | 4.4 | |
42 | 83 | 88 | G | 226 | 226 | K | 0.6 | |
43 | 83 | 88 | G | 227 | 227 | S | 26.2 | |
44 | 83 | 88 | G | 229 | 229 | Y | 4.5 |
Sequence alignments
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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: d2b0zb1; Mitochondrial cytochrome c
Alignment data:
Expectation value = 9.22e-77, Score = 224 bits (570),
Identities = 99% (107/108), Positive = 99% (107/108), Gaps = 0% (0/108).
Interface alignment data:
Interface residues in alignment: 100% (15/15).
Identities = 93% (14/15), Positive = 93% (14/15), Gaps = 0% (0/15).
Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61
TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK
d2b0zb1: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60
dssp: ---------HHHHHHHHH-------------------------E----------HHHHH-
Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109
NVLWDENNMSEYLTNPKKYIPGTKMA GGLKKEKDRNDLITYLKKACE
d2b0zb1: 61 NVLWDENNMSEYLTNPKKYIPGTKMAIGGLKKEKDRNDLITYLKKACE 108
dssp: --E----HHHHHH--HHHH-------------HHHHHHHHHHHHHH--
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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: 2b0z_A; Cytochrome c peroxidase, mitochondrial
Alignment data:
Expectation value = 0, Score = 616 bits (1588),
Identities = 100% (294/294), Positive = 100% (294/294), Gaps = 0% (0/294).
Interface alignment data:
Interface residues in alignment: 100% (17/17).
Identities = 100% (17/17), Positive = 100% (17/17), Gaps = 0% (0/17).
Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127
TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH
2b0z_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 60
dssp: -----EE--------HHHHHHHHHHHHHHHHH---HHHH---HHHHHHHHHH-----E--
Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187
DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ
2b0z_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120
dssp: --E----------HHHH--HHH---HHHHHHH-----------HHHHHHHHHHHHHHH--
Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247
GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT
2b0z_A: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 180
dssp: -----E--------HHH-------------HHHHHHHHH-----HHHHHHHHHHHH--EE
Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307
HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ
2b0z_A: 181 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240
dssp: -HHHH---EE----------HHHHHHHH---EEEE-----EEEE-----EE-HHHH----
Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361
DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL
2b0z_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294
dssp: -HHHHHHHHHHHH-HHHHHHHHHHHHHHHH---EE--------E----------