Interaction between Cytochrome c iso-1 (2b12_B) and Cytochrome c peroxidase, mitochondrial (2b12_A)
PDB and SCOP data
PDB ID: 2b12 (all binary interactions in this PDB entry)
Title: Crystal structure of the protein-protein complex between F82Y cytochrome c and cytochrome c peroxidase
Release date: 2005-10-25
Resolution: 3.0 Å
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Chain A: 2b12_B
Title: Cytochrome c iso-1
Source organism: Saccharomyces cerevisiae
Number of residues: 108
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Chain B: 2b12_A
Title: Cytochrome c peroxidase, mitochondrial
Source organism: Saccharomyces cerevisiae
Number of residues: 294
SCOP family: a.93.1.1
Structural properties
Hetero-dimer interface properties
Buried interface area: 371.91 Å2
Number of inter-residue contacts at the interface: 39
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 2b12_B
No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, % 1 49 54 T 3.1 11.1 % 2 50 55 D 3.1 3.3 % 3 51 56 A 7.8 30.1 % 4 70 75 N 20.7 37.0 % 5 72 77 K 88.4 94.7 % 6 73 78 K 45.7 26.9 % 7 76 81 P 53.2 65.0 % 8 77 82 G 52.9 95.7 % 9 78 83 T 7.2 93.1 % 10 79 84 K 18.9 19.2 % 11 81 86 A 33.8 53.4 % 12 82 87 Y 4.7 12.9 % 13 83 88 G 32.5 55.0 %
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Interface residues in 2b12_A
No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, % 1 193 193 A 49.6 91.2 % 2 194 194 A 33.1 90.6 % 3 195 195 N 12.1 46.4 % 4 197 197 V 24.7 52.1 % 5 199 199 T 29.1 77.8 % 6 200 200 N 8.8 65.3 % 7 201 201 E 30.1 96.3 % 8 204 204 L 49.2 78.1 % 9 205 205 N 13.4 94.9 % 10 208 208 N 26.3 23.8 % 11 209 209 E 12.1 26.2 % 12 227 227 S 23.3 33.1 % 13 229 229 Y 38.2 79.1 % 14 253 253 N 1.9 1.3 % 15 255 255 Q 17.4 27.2 % 16 256 256 D 2.6 2.4 %
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 |
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1 | 49 | 54 | T | 255 | 255 | Q | 3.1 | |
2 | 50 | 55 | D | 255 | 255 | Q | 0.4 | |
3 | 50 | 55 | D | 256 | 256 | D | 2.6 | |
4 | 51 | 56 | A | 199 | 199 | T | <0.1 | |
5 | 51 | 56 | A | 255 | 255 | Q | 7.7 | |
6 | 70 | 75 | N | 193 | 193 | A | 11.9 | |
7 | 70 | 75 | N | 229 | 229 | Y | 8.8 | |
8 | 72 | 77 | K | 193 | 193 | A | 12.2 | |
9 | 72 | 77 | K | 194 | 194 | A | 9.1 | |
10 | 72 | 77 | K | 201 | 201 | E | 20.3 | |
11 | 72 | 77 | K | 204 | 204 | L | 12.4 | |
12 | 72 | 77 | K | 205 | 205 | N | 13.4 | |
13 | 72 | 77 | K | 209 | 209 | E | 2.0 | |
14 | 72 | 77 | K | 229 | 229 | Y | 19.0 | |
15 | 73 | 78 | K | 193 | 193 | A | 25.5 | |
16 | 73 | 78 | K | 194 | 194 | A | 8.1 | |
17 | 73 | 78 | K | 195 | 195 | N | 12.1 | |
18 | 76 | 81 | P | 194 | 194 | A | 14.9 | |
19 | 76 | 81 | P | 197 | 197 | V | 24.7 | |
20 | 76 | 81 | P | 199 | 199 | T | 13.6 | |
21 | 76 | 81 | P | 255 | 255 | Q | <0.1 | |
22 | 77 | 82 | G | 194 | 194 | A | 1.0 | |
23 | 77 | 82 | G | 199 | 199 | T | 15.5 | |
24 | 77 | 82 | G | 200 | 200 | N | 8.8 | |
25 | 77 | 82 | G | 201 | 201 | E | 9.7 | |
26 | 77 | 82 | G | 204 | 204 | L | 11.8 | |
27 | 77 | 82 | G | 255 | 255 | Q | 6.1 | |
28 | 78 | 83 | T | 201 | 201 | E | 0.1 | |
29 | 78 | 83 | T | 204 | 204 | L | 7.1 | |
30 | 79 | 84 | K | 204 | 204 | L | 17.0 | |
31 | 79 | 84 | K | 253 | 253 | N | 1.9 | |
32 | 81 | 86 | A | 204 | 204 | L | 0.9 | |
33 | 81 | 86 | A | 208 | 208 | N | 26.3 | |
34 | 81 | 86 | A | 209 | 209 | E | 6.6 | |
35 | 82 | 87 | Y | 209 | 209 | E | 2.4 | |
36 | 82 | 87 | Y | 229 | 229 | Y | 2.3 | |
37 | 83 | 88 | G | 209 | 209 | E | 1.0 | |
38 | 83 | 88 | G | 227 | 227 | S | 23.3 | |
39 | 83 | 88 | G | 229 | 229 | Y | 8.1 |
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: 2b12_B; Cytochrome c iso-1
Alignment data:
Expectation value = 4.72e-77, Score = 225 bits (572),
Identities = 99% (107/108), Positive = 100% (108/108), Gaps = 0% (0/108).
Interface alignment data:
Interface residues in alignment: 100% (13/13).
Identities = 92% (12/13), Positive = 100% (13/13), Gaps = 0% (0/13).
Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61
TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK
2b12_B: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60
dssp: -----------HHHHHHH-----E-----------E-------E----------HHHHH-
Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109
NVLWDENNMSEYLTNPKKYIPGTKMA+GGLKKEKDRNDLITYLKKACE
2b12_B: 61 NVLWDENNMSEYLTNPKKYIPGTKMAYGGLKKEKDRNDLITYLKKACE 108
dssp: --E------HHHH--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: 2b12_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% (16/16).
Identities = 100% (16/16), Positive = 100% (16/16), Gaps = 0% (0/16).
Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127
TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH
2b12_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 60
dssp: -----EE--------HHHHHHHHHHHHHHHHH---HHHH---HHHHHHHHHH--------
Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187
DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ
2b12_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120
dssp: -------------HHHH--HHH---HHHHHHH-----------HHHHHHHHHHHHHHH--
Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247
GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT
2b12_A: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 180
dssp: -----E--------HHH-------------HHHHHHHH------HHHHHHHHHHHH--EE
Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307
HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ
2b12_A: 181 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240
dssp: --------EE----------HHHHHH-----EEEE-----EEEE-----EE-----HHHH
Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361
DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL
2b12_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294
dssp: -HHHHHHHHHHHH-HHHHHHHHHHHHHHHHH--EE--------E----------