Interaction between Cytochrome c iso-1 (2b10_B) and Cytochrome c peroxidase, mitochondrial (2b10_A)
PDB and SCOP data
PDB ID: 2b10 (all binary interactions in this PDB entry)
Title: Crystal Structure of the Protein-Protein Complex between F82S cytochrome c and cytochrome c peroxidase
Release date: 2005-10-25
Resolution: 2.8 Å
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Chain A: 2b10_B
Title: Cytochrome c iso-1
Source organism: Saccharomyces cerevisiae
Number of residues: 108
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Chain B: 2b10_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: 633.54 Å2
Number of inter-residue contacts at the interface: 51
Number of H-bonds: 1
Number of salt bridges: 3
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 2b10_B
No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, % 1 5 10 K 8.0 8.5 % 2 8 13 T 4.5 7.1 % 3 9 14 L 23.9 99.8 % 4 11 16 K 2.5 2.2 % 5 12 17 T 55.7 72.0 % 6 13 18 R 72.0 81.4 % 7 16 21 Q 50.7 50.8 % 8 17 22 C 3.6 61.3 % 9 27 32 K 41.4 32.5 % 10 28 33 V 28.0 34.2 % 11 70 75 N 20.6 38.7 % 12 72 77 K 42.5 37.1 % 13 73 78 K 33.8 21.2 % 14 81 86 A 47.7 79.4 % 15 82 87 S 21.9 83.3 % 16 83 88 G 32.5 56.5 % 17 84 89 G 1.4 12.3 % 18 85 90 L 3.8 97.0 % 19 86 91 K 59.0 46.4 % 20 87 92 K 53.1 39.8 % 21 90 95 D 26.8 79.7 %
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Interface residues in 2b10_A
No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, % 1 31 31 R 54.5 49.3 % 2 32 32 E 26.0 25.3 % 3 34 34 D 56.6 81.0 % 4 35 35 E 15.4 13.0 % 5 38 38 N 40.8 29.6 % 6 39 39 Y 103.7 78.6 % 7 120 120 Q 52.1 43.9 % 8 192 192 G 0.2 13.1 % 9 193 193 A 41.3 97.6 % 10 194 194 A 18.7 80.2 % 11 195 195 N 14.6 45.4 % 12 196 196 N 31.6 55.8 % 13 197 197 V 39.2 97.7 % 14 199 199 T 19.5 50.0 % 15 201 201 E 4.8 18.0 % 16 226 226 K 7.1 3.8 % 17 227 227 S 30.2 52.9 % 18 229 229 Y 25.4 66.5 % 19 290 290 E 51.8 36.9 % 20 294 294 L <0.1 0.0 %
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 | 5 | 10 | K | 35 | 35 | E | 2.6 | |
2 | 5 | 10 | K | 39 | 39 | Y | 5.4 | |
3 | 8 | 13 | T | 39 | 39 | Y | 4.5 | |
4 | 9 | 14 | L | 39 | 39 | Y | 23.9 | |
5 | 11 | 16 | K | 38 | 38 | N | 2.5 | |
6 | 12 | 17 | T | 38 | 38 | N | 38.3 | |
7 | 12 | 17 | T | 39 | 39 | Y | 17.4 | |
8 | 13 | 18 | R | 34 | 34 | D | 17.2 | Salt bridge |
9 | 13 | 18 | R | 39 | 39 | Y | 41.2 | |
10 | 13 | 18 | R | 196 | 196 | N | 13.7 | |
11 | 16 | 21 | Q | 192 | 192 | G | 0.2 | |
12 | 16 | 21 | Q | 193 | 193 | A | 27.4 | |
13 | 16 | 21 | Q | 195 | 195 | N | 14.6 | |
14 | 16 | 21 | Q | 227 | 227 | S | 0.9 | |
15 | 16 | 21 | Q | 229 | 229 | Y | 7.6 | |
16 | 17 | 22 | C | 193 | 193 | A | 3.6 | |
17 | 27 | 32 | K | 226 | 226 | K | 7.1 | |
18 | 27 | 32 | K | 227 | 227 | S | 29.3 | |
19 | 27 | 32 | K | 229 | 229 | Y | 5.0 | |
20 | 28 | 33 | V | 193 | 193 | A | 10.4 | |
21 | 28 | 33 | V | 201 | 201 | E | 4.8 | |
22 | 28 | 33 | V | 229 | 229 | Y | 12.8 | |
23 | 70 | 75 | N | 120 | 120 | Q | 2.6 | |
24 | 70 | 75 | N | 290 | 290 | E | 18.0 | H-bond |
25 | 72 | 77 | K | 120 | 120 | Q | 27.0 | |
26 | 72 | 77 | K | 197 | 197 | V | 7.0 | |
27 | 72 | 77 | K | 199 | 199 | T | 8.6 | |
28 | 73 | 78 | K | 290 | 290 | E | 33.8 | Salt bridge |
29 | 81 | 86 | A | 194 | 194 | A | 18.7 | |
30 | 81 | 86 | A | 196 | 196 | N | 0.1 | |
31 | 81 | 86 | A | 197 | 197 | V | 18.0 | |
32 | 81 | 86 | A | 199 | 199 | T | 10.9 | |
33 | 82 | 87 | S | 120 | 120 | Q | 9.5 | |
34 | 82 | 87 | S | 196 | 196 | N | 3.2 | |
35 | 82 | 87 | S | 197 | 197 | V | 9.3 | |
36 | 83 | 88 | G | 120 | 120 | Q | 13.1 | |
37 | 83 | 88 | G | 196 | 196 | N | 14.6 | |
38 | 83 | 88 | G | 197 | 197 | V | 4.9 | |
39 | 84 | 89 | G | 34 | 34 | D | 1.4 | |
40 | 85 | 90 | L | 34 | 34 | D | 2.6 | |
41 | 85 | 90 | L | 39 | 39 | Y | 1.2 | |
42 | 86 | 91 | K | 31 | 31 | R | 50.4 | |
43 | 86 | 91 | K | 34 | 34 | D | 8.6 | |
44 | 86 | 91 | K | 294 | 294 | L | <0.1 | |
45 | 87 | 92 | K | 31 | 31 | R | 4.1 | |
46 | 87 | 92 | K | 32 | 32 | E | 26.0 | |
47 | 87 | 92 | K | 34 | 34 | D | 15.8 | Salt bridge |
48 | 87 | 92 | K | 35 | 35 | E | 7.2 | |
49 | 90 | 95 | D | 34 | 34 | D | 11.0 | |
50 | 90 | 95 | D | 35 | 35 | E | 5.6 | |
51 | 90 | 95 | D | 39 | 39 | Y | 10.2 |
Ligands at the interaction interface
Chain | Protein | Residue no. | Ligand name | Contact area with same domain | Contact area with other domain |
---|---|---|---|---|---|
A | 2b10_B | 409 | HEM | 634.1 | 29.8 |
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: 2b10_B; Cytochrome c iso-1
Alignment data:
Expectation value = 2.08e-76, Score = 223 bits (567),
Identities = 99% (107/108), Positive = 99% (107/108), Gaps = 0% (0/108).
Interface alignment data:
Interface residues in alignment: 100% (21/21).
Identities = 95% (20/21), Positive = 95% (20/21), Gaps = 0% (0/21).
Query: 2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 61
TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK
2b10_B: 1 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK 60
dssp: ----------HHHHHHHH-------------------------E----------HHHHH-
Query: 62 NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109
NVLWDENNMSEYLTNPKKYIPGTKMA GGLKKEKDRNDLITYLKKACE
2b10_B: 61 NVLWDENNMSEYLTNPKKYIPGTKMASGGLKKEKDRNDLITYLKKACE 108
dssp: --E--HHHHHHHHH-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: 2b10_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% (20/20).
Identities = 100% (20/20), Positive = 100% (20/20), Gaps = 0% (0/20).
Query: 68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 127
TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH
2b10_A: 1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH 60
dssp: ------E--------HHHHHHHHHHHHHHHHH---HHHH---HHHHHHHHHHHH------
Query: 128 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 187
DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ
2b10_A: 61 DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ 120
dssp: ---------HHH-HHHH--HHH---HHHHHHHHHHH-------HHHHHHHHHHHHHHH--
Query: 188 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 247
GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT
2b10_A: 121 GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT 180
dssp: -----E--------HHH-------------HHHHHHHHHHH---HHHHHHHHHHHH--EE
Query: 248 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 307
HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ
2b10_A: 181 HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ 240
dssp: -HHHH---EE----------HHHHHHHH---EEEE-----EEEE-----EE-HHHHHHHH
Query: 308 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361
DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL
2b10_A: 241 DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294
dssp: -HHHHHHHHHHHH-HHHHHHHHHHHHHHHHH---E--------E-----HHH--