Cytochrome c iso-1
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain A； UniProt 3–109 Chain B； UniProt 3–109 Chain C； UniProt 3–109 Chain D； UniProt 3–109 | Not recorded | HEC HEME C × 4 ZN ZINC ION × 33 80M sulfonato-thiacalix[4]arene × 6 PO4 PHOSPHATE ION × 6 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；20% PEG 3350, 100 mM sodium acetate pH 5.6, 30 mM zinc acetate | Resolution 2.37 Å R-free 0.253 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 7PR3 | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1CHH STRUCTURAL STUDIES OF THE ROLES OF RESIDUES 82 AND 85 AT THE INTERACTIVE FACE OF CYTOCHROME C Deposited 1994-06-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 HEC HEME C × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.97 Å |
| 1CHI STRUCTURAL STUDIES OF THE ROLES OF RESIDUES 82 AND 85 AT THE INTERACTIVE FACE OF CYTOCHROME C Deposited 1994-06-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 HEC HEME C × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.00 Å |
| 1CHJ STRUCTURAL STUDIES OF THE ROLES OF RESIDUES 82 AND 85 AT THE INTERACTIVE FACE OF CYTOCHROME C Deposited 1994-06-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 HEC HEME C × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.90 Å |
| 1CIE STRUCTURAL AND FUNCTIONAL EFFECTS OF MULTIPLE MUTATIONS AT DISTAL SITES IN CYTOCHROME C Deposited 1994-09-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 HEC HEME C × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å |
| 1CIF STRUCTURAL AND FUNCTIONAL EFFECTS OF MULTIPLE MUTATIONS AT DISTAL SITES IN CYTOCHROME C Deposited 1994-09-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 HEC HEME C × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.90 Å |
| 1CIG STRUCTURAL AND FUNCTIONAL EFFECTS OF MULTIPLE MUTATIONS AT DISTAL SITES IN CYTOCHROME C Deposited 1994-09-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 HEC HEME C × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å |
| 1CIH STRUCTURAL AND FUNCTIONAL EFFECTS OF MULTIPLE MUTATIONS AT DISTAL SITES IN CYTOCHROME C Deposited 1994-09-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 HEC HEME C × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å |
| 1CRG THE ROLE OF A CONSERVED INTERNAL WATER MOLECULE AND ITS ASSOCIATED HYDROGEN BOND NETWORK IN CYTOCHROME C Deposited 1993-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 HEC HEME C × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.00 Å |
| 1CRH THE ROLE OF A CONSERVED INTERNAL WATER MOLECULE AND ITS ASSOCIATED HYDROGEN BOND NETWORK IN CYTOCHROME C Deposited 1993-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 HEC HEME C × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.90 Å |
| 1CRI THE ROLE OF A CONSERVED INTERNAL WATER MOLECULE AND ITS ASSOCIATED HYDROGEN BOND NETWORK IN CYTOCHROME C Deposited 1993-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.00 Å |
| 1CRJ THE ROLE OF A CONSERVED INTERNAL WATER MOLECULE AND ITS ASSOCIATED HYDROGEN BOND NETWORK IN CYTOCHROME C Deposited 1993-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 HEC HEME C × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.05 Å |
| 1CSU REPLACEMENTS IN A CONSERVED LEUCINE CLUSTER IN THE HYDROPHOBIC HEME POCKET OF CYTOCHROME C Deposited 1994-10-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 HEC HEME C × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.81 Å |
| 1CSV REPLACEMENTS IN A CONSERVED LEUCINE CLUSTER IN THE HYDROPHOBIC HEME POCKET OF CYTOCHROME C Deposited 1994-10-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 HEC HEME C × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.90 Å |
| 1CSW REPLACEMENTS IN A CONSERVED LEUCINE CLUSTER IN THE HYDROPHOBIC HEME POCKET OF CYTOCHROME C Deposited 1994-10-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 HEC HEME C × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.90 Å |
| 1CSX REPLACEMENTS IN A CONSERVED LEUCINE CLUSTER IN THE HYDROPHOBIC HEME POCKET OF CYTOCHROME C Deposited 1994-10-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 HEC HEME C × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.90 Å |
| 1CTY MUTATION OF TYROSINE-67 IN CYTOCHROME C SIGNIFICANTLY ALTERS THE LOCAL HEME ENVIRONMENT Deposited 1993-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 HEC HEME C × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.20 Å |
| 1CTZ MUTATION OF TYROSINE-67 IN CYTOCHROME C SIGNIFICANTLY ALTERS THE LOCAL HEME ENVIRONMENT Deposited 1993-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 HEC HEME C × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.90 Å |
| 1FHB THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE CYANIDE ADDUCT OF A MET80ALA VARIANT OF SACCHAROMYCES CEREVISIAE ISO-1-CYTOCHROME C. IDENTIFICATION OF LIGAND-RESIDUE INTERACTIONS IN THE DISTAL HEME CAVITY Deposited 1995-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–108（108 aa）
|
Mutation：H39Q, M80A, C102S Non-standard monomer：Yes (specific site not provided by mmCIF) | CYN CYANIDE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 | SOLUTION NMR mmCIF provides none of the parsed conditions | Resolution not provided |
| 1IRV CYTOCHROME C ISOZYME 1, REDUCED, MUTANT WITH ILE 75 REPLACED BY MET AND CYS 102 REPLACED BY THR Deposited 1996-06-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–108（108 aa）
|
Mutation：I75M, C102T Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.90 Å |
| 1IRW CYTOCHROME C ISOZYME 1, REDUCED, MUTANT WITH ASN 52 REPLACED BY ALA AND CYS 102 REPLACED BY THR Deposited 1996-06-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–108（108 aa）
|
Mutation：N52A, C102T Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.00 Å |
| 1KYO YEAST CYTOCHROME BC1 COMPLEX WITH BOUND SUBSTRATE CYTOCHROME C Deposited 2002-02-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric |
Chain W
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEC HEME C × 7 SMA STIGMATELLIN A × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG4000, 20 mM Tris, 0.05 % Undecyl-maltopyranoside, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.97 Å R-free 0.268 |
| 1LMS Structural model for an alkaline form of ferricytochrome c Deposited 2002-05-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–108（108 aa）
|
Mutation：K72A,K79A,C102T | HEC HEME C × 1 |
SOLUTION NMR
NMR measurement conditions
pH 11.1；298 K；Ionic strength (raw mmCIF value) 50 mM phosphate；Pressure 1
NMR sample composition
2mM protein | 50 mM phosphate buffer; 90% H2O, 10% D2O; pH 11.1
|
Resolution not provided |
| 1NMI Solution structure of the imidazole complex of iso-1 cytochrome c Deposited 2003-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–108（108 aa）
|
Not recorded | IMD IMIDAZOLE × 1 HEC HEME C × 1 |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K
NMR sample composition
1mM iso-1 cytochrome c, 120mM d5imidazole | H2O
NMR sample composition
1mM 15N labeled iso-1 cytochrome c, 120mM d5imidazole | H2O
|
Resolution not provided |
| 1RAP THE STRUCTURE AND FUNCTION OF OMEGA LOOP A REPLACEMENTS IN CYTOCHROME C Deposited 1992-08-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.25 Å |
| 1RAQ THE STRUCTURE AND FUNCTION OF OMEGA LOOP A REPLACEMENTS IN CYTOCHROME C Deposited 1992-08-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 HEC HEME C × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.90 Å |
| 1S6V Structure of a cytochrome c peroxidase-cytochrome c site specific cross-link Deposited 2004-01-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–108（107 aa）
|
Mutation：A81C, C102T | IOD IODIDE ION × 1 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；PEG 3350, KI, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 1.88 Å R-free 0.243 |
| 1S6V Structure of a cytochrome c peroxidase-cytochrome c site specific cross-link Deposited 2004-01-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
2–108（107 aa）
|
Mutation：A81C, C102T | HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；PEG 3350, KI, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 1.88 Å R-free 0.243 |
| 1U74 Electron Transfer Complex between cytochrome C and cytochrome C peroxidase Deposited 2004-08-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–108（108 aa）
|
Mutation：C102S | PO4 PHOSPHATE ION × 1 ZNH PROTOPORPHYRIN IX CONTAINING ZN × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 3350, sodium chloride, n-octyl-beta-D-glucoside, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 2.40 Å R-free 0.287 |
| 1U74 Electron Transfer Complex between cytochrome C and cytochrome C peroxidase Deposited 2004-08-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–108（108 aa）
|
Mutation：C102S | PO4 PHOSPHATE ION × 1 ZNH PROTOPORPHYRIN IX CONTAINING ZN × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 3350, sodium chloride, n-octyl-beta-D-glucoside, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 2.40 Å R-free 0.287 |
| 1YCC HIGH-RESOLUTION REFINEMENT OF YEAST ISO-1-CYTOCHROME C AND COMPARISONS WITH OTHER EUKARYOTIC CYTOCHROMES C Deposited 1990-05-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 HEC HEME C × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.23 Å |
| 1YFC Solution nmr structure of a yeast iso-1-ferrocytochrome C Deposited 1996-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–108（108 aa）
|
Mutation：C102S Non-standard monomer：Yes (specific site not provided by mmCIF) | HEC HEME C × 1 |
SOLUTION NMR
NMR measurement conditions
pH 7；303 K
|
Resolution not provided |
| 1YIC THE OXIDIZED SACCHAROMYCES CEREVISIAE ISO-1-CYTOCHROME C, NMR, 20 STRUCTURES Deposited 1997-02-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–108（108 aa）
|
Mutation：C102S Non-standard monomer：Yes (specific site not provided by mmCIF) | HEC HEME C × 1 | SOLUTION NMR mmCIF provides none of the parsed conditions | Resolution not provided |
| 2B0Z Crystal structure of the protein-protein complex between F82I cytochrome c and cytochrome c peroxidase Deposited 2005-09-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–108（108 aa）
|
Mutation：F82I | ZNH PROTOPORPHYRIN IX CONTAINING ZN × 1 HEC HEME C × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.70 Å R-free 0.289 |
| 2B10 Crystal Structure of the Protein-Protein Complex between F82S cytochrome c and cytochrome c peroxidase Deposited 2005-09-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–108（108 aa）
|
Mutation：F82S | ZNH PROTOPORPHYRIN IX CONTAINING ZN × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEG 3350, NaCl, BOG, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.80 Å R-free 0.306 |
| 2B10 Crystal Structure of the Protein-Protein Complex between F82S cytochrome c and cytochrome c peroxidase Deposited 2005-09-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–108（108 aa）
|
Mutation：F82S | ZNH PROTOPORPHYRIN IX CONTAINING ZN × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEG 3350, NaCl, BOG, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.80 Å R-free 0.306 |
| 2B11 Crystal structure of the protein-protein complex between F82W cytochrome c and cytochrome c peroxidase Deposited 2005-09-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–108（108 aa）
|
Mutation：F82W | ZNH PROTOPORPHYRIN IX CONTAINING ZN × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEG 3350, NaCl, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.30 Å R-free 0.293 |
| 2B11 Crystal structure of the protein-protein complex between F82W cytochrome c and cytochrome c peroxidase Deposited 2005-09-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–108（108 aa）
|
Mutation：F82W | HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEG 3350, NaCl, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.30 Å R-free 0.293 |
| 2B12 Crystal structure of the protein-protein complex between F82Y cytochrome c and cytochrome c peroxidase Deposited 2005-09-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–108（108 aa）
|
Mutation：F82Y | ZNH PROTOPORPHYRIN IX CONTAINING ZN × 1 HEC HEME C × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEG 3350, NaCl, BOG, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 3.02 Å R-free 0.268 |
| 2BCN Solvent isotope effects on interfacial protein electron transfer between cytochrome c and cytochrome c peroxidase Deposited 2005-10-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–108（108 aa）
|
Mutation：C107S | ZNH PROTOPORPHYRIN IX CONTAINING ZN × 2 HEC HEME C × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；295 K；PEG3350, NaCl, BOG, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 1.70 Å R-free 0.230 |
| 2GB8 Solution structure of the complex between yeast iso-1-cytochrome c and yeast cytochrome c peroxidase Deposited 2006-03-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–108（108 aa）
|
Not recorded | HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEC HEME C × 1 |
SOLUTION NMR
NMR measurement conditions
pH 6；301 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition
0.3-0.4mM Cc(Fe3+)-CcP(Fe3+), 1:1 complex; 20mM NaPi, 100mM NaCl pH 6.0 | 20mM NaPi, 100mM NaCl pH 6.0
|
Resolution not provided |
| 2HV4 NMR solution structure refinement of yeast iso-1-ferrocytochrome c Deposited 2006-07-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–108（108 aa）
|
Mutation：C102T | HEC HEME C × 1 |
SOLUTION NMR
NMR measurement conditions
pH 7；303 K；Ionic strength (raw mmCIF value) 50 mM phosphate buffer；Pressure ambient
NMR sample composition
2-3 mM cytochrome c, 50 mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition
2-3 mM cytochrome c U-15N, 50 mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition
2-3 mM cytochrome c U-15N,13C, 50 mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2JQR Solution model of crosslinked complex of cytochrome c and adrenodoxin Deposited 2007-06-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–109（108 aa）
|
Mutation：V28C, C102T | HEC HEME C × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 |
SOLUTION NMR
NMR measurement conditions
pH 7.4；285 K；Pressure ambient
NMR measurement conditions
pH 7.4；301 K；Ionic strength (raw mmCIF value) 0.4；Pressure ambient
NMR sample composition
0.4 mM [U-98% 15N] CcV28C, 0.2-0.6 mM AdxL80C, 20 mM potassium phosphate, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
0.4 mM [U-98% 15N] AdxL80C, 0.2-0.6 mM CcV28C, 20 mM potassium phosphate, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
1.0 mM [U-98% 15N] CcV28C, 5 mM DTT, 20 mM potassium phosphate, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
0.6 mM [U-98% 15N] AdxL80C, 5 mM DTT, 20 mM potassium phosphate, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 2JTI Solution structure of the yeast iso-1-cytochrome c (T12A) : yeast cytochrome c peroxidase complex Deposited 2007-08-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–109（108 aa）
|
Mutation：T12A,C102T | HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEC HEME C × 1 |
SOLUTION NMR
NMR measurement conditions
pH 6；303 K；Pressure ambient
NMR sample composition
0.3-0.4 mM [U-15N] CC, 0.3-0.4 mM CCP, 93% H2O/7% D2O | 93% H2O/7% D2O
|
Resolution not provided |
| 2LIR NMR Solution Structure of Yeast Iso-1-cytochrome c Mutant P71H in oxidized states Deposited 2011-08-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–109（108 aa）
|
Mutation：P71H, K72A, C102T | HEC HEME C × 1 |
SOLUTION NMR
NMR measurement conditions
pH 7；293 K；Ionic strength (raw mmCIF value) 50mM；Pressure ambient
NMR sample composition
1 mM entity_1-1, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1 mM entity_1-2, 100% D2O | 100% D2O
|
Resolution not provided |
| 2LIT NMR Solution Structure of Yeast Iso-1-cytochrome c Mutant P71H in reduced states Deposited 2011-08-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–109（108 aa）
|
Mutation：P71H, K72A, C102T | HEC HEME C × 1 |
SOLUTION NMR
NMR measurement conditions
pH 7；293 K；Ionic strength (raw mmCIF value) 50mM；Pressure ambient
NMR sample composition
1 mM entity_1-1, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1 mM entity_1-2, 100% D2O | 100% D2O
|
Resolution not provided |
| 2MHM Solution structure of cytochrome c Y67H Deposited 2013-11-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–109（108 aa）
|
Mutation：Y67H | HEC HEME C × 1 |
SOLUTION NMR
NMR measurement conditions
pH 7；293 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR sample composition
1 mM cytc c y67h-1, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition
1 mM cytc c y67h-2, 100% D2O | 100% D2O
|
Resolution not provided |
| 2N18 Dominant form of the low-affinity complex of yeast cytochrome c and cytochrome c peroxidase Deposited 2015-03-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
3–109（107 aa）
Fragment：UNP residues 3-109
Chain C
2–109（108 aa）
Fragment：UNP residues 2-109
|
Mutation：A81C, C102T | HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEC HEME C × 2 |
SOLUTION NMR
NMR measurement conditions
pH 6；298 K；Ionic strength (raw mmCIF value) 15；Pressure ambient
NMR sample composition
0.4 mM [U-2H; U-15N] CcP, 0.4 mM Cc, 0.4 mM Cc1, 20 mM sodium phosphate, 93% H2O/7% D2O | 93% H2O/7% D2O
|
Resolution not provided |
| 2ORL Solution structure of the cytochrome c- para-aminophenol adduct Deposited 2007-02-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–109（108 aa）
|
Mutation：C102T | HEC HEME C × 1 4NL 4-AMINOPHENOL × 1 |
SOLUTION NMR
NMR measurement conditions
pH 7；303 K；Ionic strength (raw mmCIF value) 50 mM phosphate buffer；Pressure 1
NMR sample composition
2-3mM Cytochrome c U-15N, 50mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2PCC CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ELECTRON TRANSFER PARTNERS, CYTOCHROME C PEROXIDASE AND CYTOCHROME C Deposited 1993-04-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–108（108 aa）
|
Not recorded | SO4 SULFATE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.30 Å |
| 2PCC CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ELECTRON TRANSFER PARTNERS, CYTOCHROME C PEROXIDASE AND CYTOCHROME C Deposited 1993-04-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–108（108 aa）
|
Not recorded | SO4 SULFATE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.30 Å |
| 2YCC OXIDATION STATE-DEPENDENT CONFORMATIONAL CHANGES IN CYTOCHROME C Deposited 1991-01-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–108（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 HEC HEME C × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.90 Å |
| 3CX5 Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer. Deposited 2008-04-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 23-meric |
Chain W
2–109（108 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 6PH (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate × 2 UMQ UNDECYL-MALTOSIDE × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 7 SMA STIGMATELLIN A × 2 8PE (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate × 2 9PE (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate × 2 CN5 (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate × 1 7PH (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate × 2 CN3 (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
Microbatch (paraffin oil)；pH 7.5；277 K；1M Sucrose, 10% DMSO, 20mM Tris pH 7.5, 80mM NaCl, 0.05 % UM, 1 M stigmatellin, 5% PEG 4000, Microbatch (paraffin oil), temperature 277K
|
Resolution 1.90 Å R-free 0.263 |
| 3TYI Crystal Structure of Cytochrome c - p-Sulfonatocalix[4]arene Complexes Deposited 2011-09-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–109（108 aa）
|
Mutation：C102T | HEM PROTOPORPHYRIN IX CONTAINING FE × 1 T3Y 25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9,13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；293.15 K；26 % PEG 8000, 100 mM Magnesium Chloride, 50 mM Sodium Chloride, 50 mM Sodium Cacodylate pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
|
Resolution 1.40 Å R-free 0.198 |
| 3TYI Crystal Structure of Cytochrome c - p-Sulfonatocalix[4]arene Complexes Deposited 2011-09-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–109（108 aa）
|
Mutation：C102T | HEM PROTOPORPHYRIN IX CONTAINING FE × 1 T3Y 25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9,13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；293.15 K；26 % PEG 8000, 100 mM Magnesium Chloride, 50 mM Sodium Chloride, 50 mM Sodium Cacodylate pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
|
Resolution 1.40 Å R-free 0.198 |
| 4MU8 Crystal structure of an oxidized form of yeast iso-1-cytochrome c at pH 8.8 Deposited 2013-09-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–109（108 aa）
|
Mutation：K78A, C108S | HEC HEME C × 1 SO4 SULFATE ION × 4 TBU TERTIARY-BUTYL ALCOHOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.8；293 K；90% ammonia sulfate, 0.1 M Tris-HCl (pH 8.8), 4% tert-butanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.45 Å R-free 0.154 |
| 4MU8 Crystal structure of an oxidized form of yeast iso-1-cytochrome c at pH 8.8 Deposited 2013-09-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–109（108 aa）
|
Mutation：K78A, C108S | HEC HEME C × 1 SO4 SULFATE ION × 4 TBU TERTIARY-BUTYL ALCOHOL × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.8；293 K；90% ammonia sulfate, 0.1 M Tris-HCl (pH 8.8), 4% tert-butanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.45 Å R-free 0.154 |
| 4N0K Atomic resolution crystal structure of a cytochrome c-calixarene complex Deposited 2013-10-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–107（106 aa）
|
Mutation：R13E | HEC HEME C × 1 T3Y 25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9,13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293.15 K；18 % PEG 8000, 50 mM NaCl, 100 mM MgCl2, 50 mM sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
|
Resolution 1.05 Å R-free 0.180 |
| 4N0K Atomic resolution crystal structure of a cytochrome c-calixarene complex Deposited 2013-10-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–107（106 aa）
|
Mutation：R13E | HEC HEME C × 1 T3Y 25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9,13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293.15 K；18 % PEG 8000, 50 mM NaCl, 100 mM MgCl2, 50 mM sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
|
Resolution 1.05 Å R-free 0.180 |
| 4P4Q Complex of yeast cytochrome c peroxidase (W191F) with iso-1 cytochrome c Deposited 2014-03-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
7–109（103 aa）
Fragment：UNP residues 7-109
|
Not recorded | HEM PROTOPORPHYRIN IX CONTAINING FE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；PEG 3350 15-15%, 100 mM NaAcetate, 175 mM NaCl
|
Resolution 2.01 Å R-free 0.278 |
| 4P4Q Complex of yeast cytochrome c peroxidase (W191F) with iso-1 cytochrome c Deposited 2014-03-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
7–109（103 aa）
Fragment：UNP residues 7-109
|
Not recorded | HEM PROTOPORPHYRIN IX CONTAINING FE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；PEG 3350 15-15%, 100 mM NaAcetate, 175 mM NaCl
|
Resolution 2.01 Å R-free 0.278 |
| 4Q5P Lysine-Ligated Yeast Iso-1 Cytochrome C Deposited 2014-04-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
4–109（106 aa）
Fragment：UNP residues 7-109
|
Mutation：T78C, K79G | HEM PROTOPORPHYRIN IX CONTAINING FE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.2 M ammonium phosphate, pH 8.1, 30% w/v PEG300, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.87 Å R-free 0.204 |
| 4Q5P Lysine-Ligated Yeast Iso-1 Cytochrome C Deposited 2014-04-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
4–109（106 aa）
Fragment：UNP residues 7-109
|
Mutation：T78C, K79G | HEM PROTOPORPHYRIN IX CONTAINING FE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.2 M ammonium phosphate, pH 8.1, 30% w/v PEG300, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.87 Å R-free 0.204 |
| 4Q5P Lysine-Ligated Yeast Iso-1 Cytochrome C Deposited 2014-04-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
4–109（106 aa）
Fragment：UNP residues 7-109
|
Mutation：T78C, K79G | HEM PROTOPORPHYRIN IX CONTAINING FE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.2 M ammonium phosphate, pH 8.1, 30% w/v PEG300, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.87 Å R-free 0.204 |
| 4QAO Lysine-ligated cytochrome c with F82H Deposited 2014-05-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
4–107（104 aa）
Fragment：UNP residues 8-109
|
Mutation：T78C, K79G, F82H | HEM PROTOPORPHYRIN IX CONTAINING FE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；28% w/v PEG, 0.3 M ammonium phosphate, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.10 Å R-free 0.223 |
| 4QAO Lysine-ligated cytochrome c with F82H Deposited 2014-05-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
4–107（104 aa）
Fragment：UNP residues 8-109
|
Mutation：T78C, K79G, F82H | HEM PROTOPORPHYRIN IX CONTAINING FE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；28% w/v PEG, 0.3 M ammonium phosphate, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.10 Å R-free 0.223 |
| 4QAO Lysine-ligated cytochrome c with F82H Deposited 2014-05-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
4–107（104 aa）
Fragment：UNP residues 8-109
|
Mutation：T78C, K79G, F82H | HEM PROTOPORPHYRIN IX CONTAINING FE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；28% w/v PEG, 0.3 M ammonium phosphate, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.10 Å R-free 0.223 |
| 4YE1 A cytochrome c plus calixarene structure - alternative ligand binding mode Deposited 2015-02-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–109（108 aa）
|
Mutation：R13E | HEC HEME C × 1 T3Y 25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9,13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293.15 K；18 % PEG 8000, 50 mM NaCl, 100 mM MgCl2, 50 mM sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
|
Resolution 1.39 Å R-free 0.160 |
| 4YE1 A cytochrome c plus calixarene structure - alternative ligand binding mode Deposited 2015-02-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–109（108 aa）
|
Mutation：R13E | HEC HEME C × 1 T3Y 25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9,13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293.15 K；18 % PEG 8000, 50 mM NaCl, 100 mM MgCl2, 50 mM sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
|
Resolution 1.39 Å R-free 0.160 |
| 5CIB Complex of yeast cytochrome c peroxidase (W191G) bound to 2,4-dimethylaniline with iso-1 cytochrome c Deposited 2015-07-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
2–109（108 aa）
Fragment：iso-1 cytochrome c
Chain D
2–109（108 aa）
Fragment：iso-1 cytochrome c
|
Not recorded | HEC HEME C × 4 51S 2,4-dimethylaniline × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；PEG 3350 15-15%, 100 mM NaAcetate, 175 mM NaCl
|
Resolution 3.01 Å R-free 0.304 |
| 5CIC Complex of yeast cytochrome c peroxidase (W191G) bound to 3-aminobenzotrifluoride with iso-1 cytochrome c Deposited 2015-07-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
2–109（108 aa）
Chain D
2–109（108 aa）
|
Not recorded | HEC HEME C × 4 51R 3-(trifluoromethyl)aniline × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；PEG 3350 15-15%, 100 mM NaAcetate, 175 mM NaCl
|
Resolution 2.10 Å R-free 0.228 |
| 5CID Complex of yeast cytochrome c peroxidase (W191G) bound to o-toluidine with iso-1 cytochrome c Deposited 2015-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
2–109（108 aa）
Chain D
2–109（108 aa）
|
Not recorded | HEC HEME C × 4 51V 2-methylaniline × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；PEG 3350 15-15%, 100 mM NaAcetate, 175 mM NaCl
|
Resolution 2.76 Å R-free 0.268 |
| 5CIE Complex of yeast cytochrome c peroxidase (W191G) bound to aniline with iso-1 cytochrome c Deposited 2015-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
2–109（108 aa）
Chain D
2–109（108 aa）
|
Not recorded | HEC HEME C × 4 ANL ANILINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；PEG 3350 15-15%, 100 mM NaAcetate, 175 mM NaCl
|
Resolution 2.60 Å R-free 0.294 |
| 5CIF Complex of yeast cytochrome c peroxidase (W191F) with iso-1 cytochrome c Deposited 2015-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
7–109（103 aa）
|
Not recorded | HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；PEG 3350 15-15%, 100 mM NaAcetate, 175 mM NaCl
|
Resolution 2.01 Å R-free 0.268 |
| 5CIF Complex of yeast cytochrome c peroxidase (W191F) with iso-1 cytochrome c Deposited 2015-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
7–109（103 aa）
|
Not recorded | HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；PEG 3350 15-15%, 100 mM NaAcetate, 175 mM NaCl
|
Resolution 2.01 Å R-free 0.268 |
| 5CIG Complex of yeast cytochrome c peroxidase (W191G) with iso-1 cytochrome c Deposited 2015-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–109（108 aa）
|
Not recorded | HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；PEG 3350 15-15%, 100 mM NaAcetate, 175 mM NaCl
|
Resolution 2.06 Å R-free 0.298 |
| 5CIG Complex of yeast cytochrome c peroxidase (W191G) with iso-1 cytochrome c Deposited 2015-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
2–109（108 aa）
|
Not recorded | HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；PEG 3350 15-15%, 100 mM NaAcetate, 175 mM NaCl
|
Resolution 2.06 Å R-free 0.298 |
| 5CIH Complex of yeast cytochrome c peroxidase (W191Y) with iso-1 cytochrome c Deposited 2015-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
7–109（103 aa）
|
Not recorded | HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；PEG 3350 15-15%, 100 mM NaAcetate, 175 mM NaCl
|
Resolution 2.60 Å R-free 0.310 |
| 5CIH Complex of yeast cytochrome c peroxidase (W191Y) with iso-1 cytochrome c Deposited 2015-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
7–109（103 aa）
|
Not recorded | HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；PEG 3350 15-15%, 100 mM NaAcetate, 175 mM NaCl
|
Resolution 2.60 Å R-free 0.310 |
| 5KKE Crystal Structure of a Domain-swapped Dimer of Yeast Iso-1-cytochrome c with CYMAL5 Deposited 2016-06-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
2–109（108 aa）
|
Mutation：K72A, C102S | HEC HEME C × 2 SO4 SULFATE ION × 4 CM5 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE × 2 CL CHLORIDE ION × 2 GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；Reservior solution: 77% Ammonium Sulfate, 0.1 M Tris, pH 7.5
Protein Solution: 18 mg/mL in 75 % Ammonium Sulfate
Detergent Solution: 2.5 mM CYMAL-5 in deionized water
Mixed 2:2:1
|
Resolution 1.70 Å R-free 0.204 |
| 5KLU Crystal Structure of a Domain-swapped Dimer of Yeast Iso-1-cytochrome c with omega-undecylenyl-beta-D-maltopyranoside Deposited 2016-06-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
4–109（106 aa）
Chain B
4–109（106 aa）
|
Mutation：K72A, C102S Mutation：K72A, C102S | HEC HEME C × 2 6UZ omega-undecylenyl-beta-D-maltopyranoside × 2 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；Reservior: 90% ammonium sulfate, 0.1 M Tris, pH 7.5
Protein: 8 mg/mL in 75% ammonium sulfate
Detergent: 12 mM w-undecylenyl-b-D-maltopyranoside in deionized water
Mixed 2:2:1
|
Resolution 1.99 Å R-free 0.256 |
| 5KPF Crystal structure of cytochrome c - Phenyl-trisulfonatocalix[4]arene complex Deposited 2016-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–109（107 aa）
|
Not recorded | HEC HEME C × 1 NO3 NITRATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；20 mM PEG 3350, 200 mM Ammonium Nitrate pH 6.3
cyt c-sclx4 seed (grown in 18% PEG 8000, 50 mM NaCl, 100 mM MgCl2, 50 mM NaOAc pH 5.6)
|
Resolution 1.70 Å R-free 0.207 |
| 5KPF Crystal structure of cytochrome c - Phenyl-trisulfonatocalix[4]arene complex Deposited 2016-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
3–109（107 aa）
|
Not recorded | HEC HEME C × 1 6VJ Phenyl-trisulfonatocalix[4]arene × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；20 mM PEG 3350, 200 mM Ammonium Nitrate pH 6.3
cyt c-sclx4 seed (grown in 18% PEG 8000, 50 mM NaCl, 100 mM MgCl2, 50 mM NaOAc pH 5.6)
|
Resolution 1.70 Å R-free 0.207 |
| 5LFT Crystal structure of cytochrome c - Bromo-trisulfonatocalix[4]arene complexes Deposited 2016-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–109（107 aa）
|
Not recorded | HEC HEME C × 1 BR BROMIDE ION × 2 6VB Bromo-trisulfonatocalix[4]arene × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；30% PEG 8000, 50 mM NaCl, 100 mM MgCl2, 50 mM NaOAc pH 5.6
|
Resolution 1.25 Å R-free 0.239 |
| 5LYC Cytochrome c in complex with phosphonato-calix[6]arene Deposited 2016-09-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3–109（107 aa）
Chain B
3–109（107 aa）
|
Mutation：C102T Mutation：C102T | HEC HEME C × 2 7AZ phosphonato-calix[6]arene × 2 SO4 SULFATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；3.15M ammonium sulfate
100 mM sodium citrate pH 5.0
|
Resolution 1.80 Å R-free 0.199 |
| 5NCV Crystal Structure of Cytochrome c in complex with p-Methylphosphonatocalix[4]arene Deposited 2017-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–109（107 aa）
|
Mutation：T-5A, C102T | HEC HEME C × 1 8TE p-Methylphosphonatocalix[4]arene × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；20 % PEG 8000, 50 mM NaCl, 50 mM sodium acetate (pH 5.6). [Cytochrome c] = 0.75 mM and [Methylphosphonatocalix[4]arene] = 0.3 mM
|
Resolution 1.50 Å R-free 0.201 |
| 5NCV Crystal Structure of Cytochrome c in complex with p-Methylphosphonatocalix[4]arene Deposited 2017-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
3–109（107 aa）
|
Mutation：T-5A, C102T | HEC HEME C × 1 8TE p-Methylphosphonatocalix[4]arene × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；20 % PEG 8000, 50 mM NaCl, 50 mM sodium acetate (pH 5.6). [Cytochrome c] = 0.75 mM and [Methylphosphonatocalix[4]arene] = 0.3 mM
|
Resolution 1.50 Å R-free 0.201 |
| 5T7H Crystal structure of dimeric yeast iso-1-cytochrome C with CYMAL6 Deposited 2016-09-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–109（109 aa）
Chain D
1–109（109 aa）
|
Mutation：K72A, C10S Mutation：K72A, C10S | SO4 SULFATE ION × 4 ZE7 6-cyclohexylhexan-1-ol × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；75% (NH4)2SO4, AN 86% (NH4)2SO4 AND
0.1 M TRIS RESERVOIR SOLUTION, AND 5.6 MM CYMAL-6., PH 7.5,
VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
|
Resolution 2.00 Å R-free 0.248 |
| 5T7H Crystal structure of dimeric yeast iso-1-cytochrome C with CYMAL6 Deposited 2016-09-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
1–109（109 aa）
Chain C
1–109（109 aa）
|
Mutation：K72A, C10S Mutation：K72A, C10S | SO4 SULFATE ION × 5 ZE7 6-cyclohexylhexan-1-ol × 2 HEC HEME C × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；75% (NH4)2SO4, AN 86% (NH4)2SO4 AND
0.1 M TRIS RESERVOIR SOLUTION, AND 5.6 MM CYMAL-6., PH 7.5,
VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
|
Resolution 2.00 Å R-free 0.248 |
| 6EGY Crystal structure of cytochrome c in complex with mono-PEGylated sulfonatocalix[4]arene Deposited 2017-09-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–109（108 aa）
|
Mutation：C102T | HEC HEME C × 1 SO4 SULFATE ION × 1 B4T mono-PEGylated sulfonatocalix[4]arene × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.6 M sodium citrate, 0.1 M Sodium Chloride, and 0.1 M Sodium Sulfate
|
Resolution 2.70 Å R-free 0.273 |
| 6EGY Crystal structure of cytochrome c in complex with mono-PEGylated sulfonatocalix[4]arene Deposited 2017-09-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–109（108 aa）
|
Mutation：C102T | HEC HEME C × 1 B4T mono-PEGylated sulfonatocalix[4]arene × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.6 M sodium citrate, 0.1 M Sodium Chloride, and 0.1 M Sodium Sulfate
|
Resolution 2.70 Å R-free 0.273 |
| 6EGZ Crystal structure of cytochrome c in complex with di-PEGylated sulfonatocalix[4]arene Deposited 2017-09-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–109（108 aa）
|
Mutation：C102T | HEC HEME C × 1 B4X di-PEGylated sulfonatocalix[4]arene × 1 SO4 SULFATE ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.6 M Sodium Citrate, 0.1 M Sodium Chloride, 0.1 M Sodium Sulfate
|
Resolution 2.17 Å R-free 0.247 |
| 6EGZ Crystal structure of cytochrome c in complex with di-PEGylated sulfonatocalix[4]arene Deposited 2017-09-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–109（108 aa）
|
Mutation：C102T | HEC HEME C × 1 B4X di-PEGylated sulfonatocalix[4]arene × 3 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.6 M Sodium Citrate, 0.1 M Sodium Chloride, 0.1 M Sodium Sulfate
|
Resolution 2.17 Å R-free 0.247 |
| 6GD6 Cytochrome c in complex with Sulfonato-calix[8]arene, H3 form with ammonium sulfate Deposited 2018-04-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–109（107 aa）
|
Mutation：C102T, T-5A | HEC HEME C × 1 EVB sulfonato-calix[8]arene × 1 SO4 SULFATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.75 M ammonium sulfate
0.2 M NaCl
(2x protein solution : 1x crystallisation condition)
|
Resolution 1.20 Å R-free 0.136 |
| 6GD7 Cytochrome c in complex with Sulfonato-calix[8]arene, H3 form with PEG Deposited 2018-04-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–109（107 aa）
|
Mutation：C102T, T-5A | HEC HEME C × 1 EVB sulfonato-calix[8]arene × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；5 % PEG 3350
(2x protein solution : 1x crystallisation condition)
|
Resolution 1.55 Å R-free 0.183 |
| 6GD8 Cytochrome c in complex with Sulfonato-calix[8]arene, P31 form Deposited 2018-04-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–109（107 aa）
|
Mutation：C102T, T-5A | HEC HEME C × 1 EVB sulfonato-calix[8]arene × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；24 % PEG 3350
0.27 M NaCl
0.09 M MES pH 5.5
(2x protein solution : 1x crystallisation condition)
|
Resolution 2.50 Å R-free 0.200 |
| 6GD8 Cytochrome c in complex with Sulfonato-calix[8]arene, P31 form Deposited 2018-04-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
3–109（107 aa）
|
Mutation：C102T, T-5A | HEC HEME C × 1 EVB sulfonato-calix[8]arene × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；24 % PEG 3350
0.27 M NaCl
0.09 M MES pH 5.5
(2x protein solution : 1x crystallisation condition)
|
Resolution 2.50 Å R-free 0.200 |
| 6GD8 Cytochrome c in complex with Sulfonato-calix[8]arene, P31 form Deposited 2018-04-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
3–109（107 aa）
|
Mutation：C102T, T-5A | HEC HEME C × 1 EVB sulfonato-calix[8]arene × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；24 % PEG 3350
0.27 M NaCl
0.09 M MES pH 5.5
(2x protein solution : 1x crystallisation condition)
|
Resolution 2.50 Å R-free 0.200 |
| 6GD8 Cytochrome c in complex with Sulfonato-calix[8]arene, P31 form Deposited 2018-04-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
3–109（107 aa）
|
Mutation：C102T, T-5A | HEC HEME C × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；24 % PEG 3350
0.27 M NaCl
0.09 M MES pH 5.5
(2x protein solution : 1x crystallisation condition)
|
Resolution 2.50 Å R-free 0.200 |
| 6GD9 Cytochrome c in complex with Sulfonato-calix[8]arene, P43212 form Deposited 2018-04-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–109（107 aa）
|
Mutation：C102T, T-5A | HEC HEME C × 1 EVB sulfonato-calix[8]arene × 3 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 4 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.85 M ammonium sulfate
0.1 M HEPES pH 7.0
0.2 M NaCl
(2x protein solution : 1x crystallisation condition)
|
Resolution 2.65 Å R-free 0.286 |
| 6GDA Cytochrome c in complex with Sulfonato-calix[8]arene, P43212 form soaked with Spermine Deposited 2018-04-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–109（107 aa）
|
Mutation：C102T, T-5A | HEC HEME C × 1 EVB sulfonato-calix[8]arene × 3 SO4 SULFATE ION × 9 SPM SPERMINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；2.1 M ammonium sulfate
0.1 M MES pH 6.5
|
Resolution 2.80 Å R-free 0.243 |
| 6P41 Yeast cytochrome c peroxidase (W191Y:L232E) in complex with iso-1 cytochrome c Deposited 2019-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
7–109（103 aa）
|
Not recorded | HEM PROTOPORPHYRIN IX CONTAINING FE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；100 mM sodium acetate,175 mM NaCl, 5 mM n-octyl-B-D-glucoside, polyethylene glycol 3350 18%-20%
|
Resolution 2.90 Å R-free 0.273 |
| 6P41 Yeast cytochrome c peroxidase (W191Y:L232E) in complex with iso-1 cytochrome c Deposited 2019-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
7–109（103 aa）
|
Not recorded | HEM PROTOPORPHYRIN IX CONTAINING FE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；100 mM sodium acetate,175 mM NaCl, 5 mM n-octyl-B-D-glucoside, polyethylene glycol 3350 18%-20%
|
Resolution 2.90 Å R-free 0.273 |
| 6P42 Yeast cytochrome c peroxidase (W191Y:L232H) in complex with iso-1 cytochrome c Deposited 2019-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
7–109（103 aa）
|
Not recorded | HEM PROTOPORPHYRIN IX CONTAINING FE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；100 mM sodium acetate,175 mM NaCl, 5 mM n-octyl-B-D-glucoside, polyethylene glycol 3350 18%-20%, L-proline
|
Resolution 2.90 Å R-free 0.271 |
| 6P42 Yeast cytochrome c peroxidase (W191Y:L232H) in complex with iso-1 cytochrome c Deposited 2019-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
7–109（103 aa）
|
Not recorded | HEM PROTOPORPHYRIN IX CONTAINING FE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；100 mM sodium acetate,175 mM NaCl, 5 mM n-octyl-B-D-glucoside, polyethylene glycol 3350 18%-20%, L-proline
|
Resolution 2.90 Å R-free 0.271 |
| 6P43 Yeast cytochrome c peroxidase in complex with iso-1 cytochrome c (Y48K) Deposited 2019-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
2–109（108 aa）
|
Mutation：Y48K | HEM PROTOPORPHYRIN IX CONTAINING FE × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；100 mM sodium acetate, 175 mM NaCl, 5 mM n-octyl-B-D-glucoside, polyethylene glycol 3350 14%-20%
|
Resolution 1.91 Å R-free 0.228 |
| 6RGI Partially unfolded cytochrome c in complex with sulfonatocalix[6]arene Deposited 2019-04-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–109（107 aa）
|
Not recorded | HEC HEME C × 1 FWQ p-sulfonatocalix[6]arene × 1 IMD IMIDAZOLE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；11 % PEG 8000, 0.1 M imidazole, 2 mM sulfonato-calix[6]arene
|
Resolution 2.64 Å R-free 0.250 |
| 6RSI cytochrome c co-crystallized with 25 eq. sulfonato-calix[8]arene - structure 0 Deposited 2019-05-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–109（107 aa）
|
Not recorded | HEC HEME C × 1 EVB sulfonato-calix[8]arene × 3 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.10 M HEPES pH 7.5, 0.15 M NaCl, 2.20 M ammonium sulfate, 0.05 M sulfonato-calix[8]arene.
|
Resolution 2.48 Å R-free 0.199 |
| 6RSJ Cytochrome c co-crystallized with 20 eq. sulfonato-calix[8]arene and soaked with 25 eq. spermine - structure I Deposited 2019-05-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–109（107 aa）
|
Not recorded | HEC HEME C × 1 EVB sulfonato-calix[8]arene × 3 SPM SPERMINE × 2 SO4 SULFATE ION × 2 GOL GLYCEROL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.10 M HEPES pH 7.5, 0.15 M NaCl, 2.2 M Ammonium sulfate, 0.04 M sulfonato-calix[8]arene
|
Resolution 2.27 Å R-free 0.212 |
| 6RSK Cytochrome c co-crystallized with 20 eq. sulfonato-calix[8]arene and 15 eq. spermine - structure II Deposited 2019-05-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–109（107 aa）
|
Not recorded | HEC HEME C × 1 EVB sulfonato-calix[8]arene × 3 SO4 SULFATE ION × 6 SPM SPERMINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M HEPES pH 7.5, 0.15 M NaCl, 2.2 M Ammonium sulfate, 0.04 M sulfonato-calix[8]arene, 0.03 M spermine
|
Resolution 2.31 Å R-free 0.222 |
| 6RSK Cytochrome c co-crystallized with 20 eq. sulfonato-calix[8]arene and 15 eq. spermine - structure II Deposited 2019-05-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
3–109（107 aa）
|
Not recorded | HEC HEME C × 1 EVB sulfonato-calix[8]arene × 3 SO4 SULFATE ION × 5 SPM SPERMINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M HEPES pH 7.5, 0.15 M NaCl, 2.2 M Ammonium sulfate, 0.04 M sulfonato-calix[8]arene, 0.03 M spermine
|
Resolution 2.31 Å R-free 0.222 |
| 6RSL Cytochrome c co-crystallized with 10 eq. sulfonato-calix[8]arene and 25 eq. spermine (dry-coating method) - structure III Deposited 2019-05-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–109（107 aa）
|
Not recorded | HEC HEME C × 1 EVB sulfonato-calix[8]arene × 3 SPM SPERMINE × 4 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.10 M HEPES pH 7.5, 0.15 M NaCl, 2.20 M Ammonium sulfate, 0.02 M sulfonato-calix[8]arene, 0.05 M spermine
|
Resolution 1.99 Å R-free 0.265 |
| 6RSL Cytochrome c co-crystallized with 10 eq. sulfonato-calix[8]arene and 25 eq. spermine (dry-coating method) - structure III Deposited 2019-05-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
3–109（107 aa）
|
Not recorded | HEC HEME C × 1 EVB sulfonato-calix[8]arene × 3 SPM SPERMINE × 4 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.10 M HEPES pH 7.5, 0.15 M NaCl, 2.20 M Ammonium sulfate, 0.02 M sulfonato-calix[8]arene, 0.05 M spermine
|
Resolution 1.99 Å R-free 0.265 |
| 6S8Y Crystal structure of cytochrome c in complex with a sulfonated quinoline-derived foldamer Deposited 2019-07-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–109（107 aa）
|
Not recorded | HEC HEME C × 1 ZN ZINC ION × 3 ACT ACETATE ION × 2 L0T 8-acetamido-2-[[2-[[2-[[2-[[2-[[2-[[2-[(2-carboxy-4-sulfonato-quinolin-8-yl)carbamoyl]-4-sulfonato-quinolin-8-yl]carbamoyl]-4-sulfonato-quinolin-8-yl]carbamoyl]-4-sulfonato-quinolin-8-yl]carbamoyl]-4-sulfonato-quinolin-8-yl]carbamoyl]-4-sulfonato-quinolin-8-yl]carbamoyl]-4-sulfonato-quinolin-8-yl]carbamoyl]quinoline-4-sulfonate × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；5 % PEG 3350, 100 mM sodium acetate pH 4.5, 200 mM zinc acetate
|
Resolution 2.09 Å R-free 0.267 |
| 6SUY Yeast cytochrome c in complex with an octa-anionic calix[4]arene Deposited 2019-09-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
2–109（108 aa）
Chain B
2–109（108 aa）
|
Not recorded | HEC HEME C × 2 LVT octa-anionic calix[4]arene × 2 NA SODIUM ION × 2 SO4 SULFATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；3.15 M Ammonium sulfate + 0.1 M sodium citrate pH 5.0
|
Resolution 1.75 Å R-free 0.179 |
| 6Y0J Cytochrome c in complex with phosphonato-calix[6]arene and sulfonato-calix[8]arene Deposited 2020-02-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–109（107 aa）
|
Not recorded | HEC HEME C × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；10 % PEG 8000, 8 % ethylene glycol, 100 mM HEPES pH 7.5
|
Resolution 2.70 Å R-free 0.269 |
| 6Y0J Cytochrome c in complex with phosphonato-calix[6]arene and sulfonato-calix[8]arene Deposited 2020-02-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
3–109（107 aa）
|
Not recorded | HEC HEME C × 1 7AZ phosphonato-calix[6]arene × 2 EVB sulfonato-calix[8]arene × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；10 % PEG 8000, 8 % ethylene glycol, 100 mM HEPES pH 7.5
|
Resolution 2.70 Å R-free 0.269 |
| 6Y0J Cytochrome c in complex with phosphonato-calix[6]arene and sulfonato-calix[8]arene Deposited 2020-02-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
3–109（107 aa）
|
Not recorded | HEC HEME C × 1 7AZ phosphonato-calix[6]arene × 1 EVB sulfonato-calix[8]arene × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；10 % PEG 8000, 8 % ethylene glycol, 100 mM HEPES pH 7.5
|
Resolution 2.70 Å R-free 0.269 |
| 6Y0J Cytochrome c in complex with phosphonato-calix[6]arene and sulfonato-calix[8]arene Deposited 2020-02-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
3–109（107 aa）
|
Not recorded | HEC HEME C × 1 7AZ phosphonato-calix[6]arene × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；10 % PEG 8000, 8 % ethylene glycol, 100 mM HEPES pH 7.5
|
Resolution 2.70 Å R-free 0.269 |
| 7BBT Structure of cytochrome c in complex with a p-benzyl-sulfonato-calix[8]arene-PEG pseudorotaxane Deposited 2020-12-18 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
3–109（107 aa）
Chain B
3–109（107 aa）
Chain C
3–109（107 aa）
Chain D
3–109（107 aa）
|
Not recorded | HEC HEME C × 4 T8W 4-[[49,50,51,52,53,54,55,56-octahydroxy-11,17,23,29,35,41,47-heptakis[(4-sulfonatophenyl)methyl]-5-nonacyclo[43.3.1.13,7.19,13.115,19.121,25.127,31.133,37.139,43]hexapentaconta-1(49),3,5,7(56),9,11,13(55),15,17,19(54),21,23,25(53),27,29,31(52),33,35,37(51),39,41,43(50),45,47-tetracosaenyl]methyl]benzenesulfonate × 3 15P POLYETHYLENE GLYCOL (N=34) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20 % PEG 3350
200mM Ammonium formate
|
Resolution 3.02 Å R-free 0.261 |
| 7MRI Crystal structure of N63T yeast iso-1-cytochrome c Deposited 2021-05-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–109（107 aa）
|
Not recorded | HEC HEME C × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris, pH 8.5, 30% w/v PEG1000
|
Resolution 2.46 Å R-free 0.208 |
| 7MRI Crystal structure of N63T yeast iso-1-cytochrome c Deposited 2021-05-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
3–109（107 aa）
|
Not recorded | HEC HEME C × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris, pH 8.5, 30% w/v PEG1000
|
Resolution 2.46 Å R-free 0.208 |
| 7MRI Crystal structure of N63T yeast iso-1-cytochrome c Deposited 2021-05-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
3–109（107 aa）
|
Not recorded | HEC HEME C × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris, pH 8.5, 30% w/v PEG1000
|
Resolution 2.46 Å R-free 0.208 |
| 7PR2 Cocrystal of cytochrome c and sulfonato-thiacalix[4]arene Deposited 2021-09-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
3–109（107 aa）
Chain B
3–109（107 aa）
|
Not recorded | HEC HEME C × 2 80M sulfonato-thiacalix[4]arene × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；25% PEG 3350, 100 mM tri-Sodium citrate pH 5.6, 100 mM Magnesium chloride
|
Resolution 1.73 Å R-free 0.251 |
| 7PR4 Cocrystal Form II of a cytochrome c, sulfonato-thiacalix[4]arene - zinc cluster Deposited 2021-09-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–109（107 aa）
|
Not recorded | HEC HEME C × 1 80M sulfonato-thiacalix[4]arene × 1 ZN ZINC ION × 6 PO4 PHOSPHATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；20% PEG 3350, 100 mM sodium acetate pH 5.6, 10 mM zinc acetate
|
Resolution 1.32 Å R-free 0.225 |
| 9Q39 Structure of a sortase-linked cytochrome c peroxidase - cytochrome c fusion protein Deposited 2025-08-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
7–109（103 aa）
|
Not recorded | PO4 PHOSPHATE ION × 1 HEC HEME C × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；Upon purification, CcP-GGSG(2x)LPATGGG was buffer exchanged into filtered nanopure water and concentrated to 0.5 mM. Initial crystal hits were obtained using a Gryphon robot (Arts Robbins Instrument). Larger crystals were optimized via vapor diffusion in 4 microliter sitting drops, which were mixed 1:1 with well solution (14-20 % PEG 8000, 40 mM KH2PO4, 20 % glycerol, pH 3.0-5.5). Crystals growing under these conditions formed within a week.
|
Resolution 3.24 Å R-free 0.331 |
91 other PDB entries and 125 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | CYC1_YEAST |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 2–108； UniProt 3–109 Author chain B； PDBConstruct 2–108； UniProt 3–109 Author chain C； PDBConstruct 2–108； UniProt 3–109 Author chain D； PDBConstruct 2–108； UniProt 3–109 |
