3nbs

Crystal structure of dimeric cytochrome c from horse heart

Method: X-RAY DIFFRACTION D_max: 79.8 Å Quality: EXCELLENT

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome c

OrganismNot specified

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–105 Chain B； UniProt 2–105	Not recorded	HEC HEME C × 2 PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；30% PEG 200, 0.1M Tris-HCl, 0.2M ammonium phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.20 Å R-free 0.273
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 2–105 Chain D； UniProt 2–105	Not recorded	HEC HEME C × 2 PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；30% PEG 200, 0.1M Tris-HCl, 0.2M ammonium phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.20 Å R-free 0.273

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 3NBS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AKK SOLUTION STRUCTURE OF OXIDIZED HORSE HEART CYTOCHROME C, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-05-22	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 1–104（104 aa）	Not recorded	HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 7；293 K	Resolution not provided
1CRC CYTOCHROME C AT LOW IONIC STRENGTH Deposited 1995-03-22	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 1–104（104 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.08 Å
1CRC CYTOCHROME C AT LOW IONIC STRENGTH Deposited 1995-03-22	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 1–104（104 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.08 Å
1FI7 Solution structure of the imidazole complex of cytochrome C Deposited 2000-08-03	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 1–104（104 aa）	Not recorded	IMD IMIDAZOLE × 1 HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 5.7；313 K；Pressure 1 NMR sample composition 6mM cytochrome c, 1.2M Imidazole \| H2O NMR sample composition 6mM cytochrome c, 1.2M Imidazole \| D2O	Resolution not provided
1FI9 SOLUTION STRUCTURE OF THE IMIDAZOLE COMPLEX OF CYTOCHROME C Deposited 2000-08-03	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 1–104（104 aa）	Not recorded	IMD IMIDAZOLE × 1 HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 5.7；313 K；Pressure 1 NMR sample composition 6mM cytochrome c, 1.2M imidazole \| H2O NMR sample composition 6mM cytochrome c, 1.2M imidazole \| D2O	Resolution not provided
1GIW SOLUTION STRUCTURE OF REDUCED HORSE HEART CYTOCHROME C, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1998-06-17	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 1–104（104 aa）	Not recorded	HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 100 mM PHOSPHATE；Pressure 1013 NMR sample composition H2O	Resolution not provided
1HRC HIGH-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF HORSE HEART CYTOCHROME C Deposited 1994-08-16	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 1–104（104 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1I5T SOLUTION STRUCTURE OF CYANOFERRICYTOCHROME C Deposited 2001-02-28	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 1–104（104 aa）	Not recorded	CYN CYANIDE ION × 1 HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 7；303 K NMR sample composition 5mM cytochrome c,50mM potassium cyanide \| 90% H2O/10% D2O NMR sample composition 5mM cytochrome c, 50mM potassium cyanide \| D2O	Resolution not provided
1LC1 Solution Structure Of Reduced Horse Heart Cytochrome c in 30% Acetonitrile Solution, NMR Minimized Average Structure Deposited 2002-04-04	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 1–104（104 aa）	Not recorded	HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 50mM；Pressure 1 NMR sample composition 5mM FERROCYTOCHROME C 1H; 50mM PHOSPHATE BUFFER; 70% H2O, 30% CD3CN \| 70% H2O, 30% CD3CN	Resolution not provided
1LC2 Solution Structure Of Reduced Horse Heart Cytochrome c in 30% Acetonitrile Solution, NMR 30 Structures Deposited 2002-04-04	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 1–104（104 aa）	Not recorded	HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 50mM；Pressure 1 NMR sample composition 5mM FERROCYTOCHROME C 1H; 50mM PHOSPHATE BUFFER; 70% H2O, 30% CD3CN \| 70% H2O, 30% CD3CN	Resolution not provided
1M60 Solution Structure of Zinc-substituted cytochrome c Deposited 2002-07-11	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 1–104（104 aa）	Not recorded	HES ZINC SUBSTITUTED HEME C × 1	SOLUTION NMR NMR measurement conditions pH 6.5；293 K；Pressure 1 NMR sample composition 5mM Zn-cytc \| 90% H2O, 10% D2O; 90% D2O, 10% D2O	Resolution not provided
1OCD CYTOCHROME C (OXIDIZED) FROM EQUUS CABALLUS, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-07-03	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 1–104（104 aa）	Not recorded	HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 5.7；293 K NMR sample composition [U-15N] 7-10 mM cytochrome c, 50 mM potassium phosphate \| 90% H2O/10% D2O NMR sample composition [U-13C; U-15N] 15 mM cytochrome c, 50 mM potassium phosphate \| 90% H2O/10% D2O	Resolution not provided
1U75 Electron Transfer Complex between Horse Heart Cytochrome c and Zinc-Porphyrin Substituted 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 × 3 PDB declaration: trimeric	Chain B 1–104（104 aa）	Not recorded	PO4 PHOSPHATE ION × 2 ZNH PROTOPORPHYRIN IX CONTAINING ZN × 2 HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.55 Å R-free 0.306
1WEJ IGG1 FAB FRAGMENT (OF E8 ANTIBODY) COMPLEXED WITH HORSE CYTOCHROME C AT 1.8 A RESOLUTION Deposited 1998-03-26	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 F 1–104（104 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.4；50MM ZINC ACETATE BUFFER, PH 6.4, 25% (W/V) PEG 4000.	Resolution 1.80 Å R-free 0.256
1WEJ IGG1 FAB FRAGMENT (OF E8 ANTIBODY) COMPLEXED WITH HORSE CYTOCHROME C AT 1.8 A RESOLUTION Deposited 1998-03-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–104（104 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.4；50MM ZINC ACETATE BUFFER, PH 6.4, 25% (W/V) PEG 4000.	Resolution 1.80 Å R-free 0.256
2FRC CYTOCHROME C (REDUCED) FROM EQUUS CABALLUS, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-07-02	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 1–104（104 aa）	Not recorded	HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 5.7；293 K	Resolution not provided
2GIW SOLUTION STRUCTURE OF REDUCED HORSE HEART CYTOCHROME C, NMR, 40 STRUCTURES Deposited 1998-06-25	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 1–104（104 aa）	Not recorded	HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 100 mM PHOSPHATE；Pressure 1013 NMR sample composition H2O	Resolution not provided
2N3B Structure of oxidized horse heart cytochrome c encapsulated in reverse micelles Deposited 2015-05-27	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 2–105（104 aa）	Not recorded	HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Pressure ambient NMR sample composition 0.15 mM [U-100% 13C; U-100% 15N] protein, 1.5 M H2O, 25 mM sodium phosphate, 105 mM 1-decanoyl-rac-glycerol, 45 mM lauryldimethylamine-N-oxide, 8 mM hexanol, 8.67 M [U-99% 2H] pentane, Deuterated pentane \| Deuterated pentane NMR sample composition 0.15 mM [U-100% 15N] protein, 1.5 M H2O, 25 mM sodium phosphate, 105 mM 1-decanoyl-rac-glycerol, 45 mM lauryldimethylamine-N-oxide, 8 mM hexanol, 8.67 M [U-99% 2H] pentane, Deuterated pentane \| Deuterated pentane	Resolution not provided
2PCB 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 1–104（104 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
3JBT Atomic structure of the Apaf-1 apoptosome Deposited 2015-10-15	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 × 14 PDB declaration: tetradecameric	Chain B 1–105（105 aa） Chain D 1–105（105 aa） Chain F 1–105（105 aa） Chain H 1–105（105 aa） Chain J 1–105（105 aa） Chain L 1–105（105 aa） Chain N 1–105（105 aa）	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 7 HEM PROTOPORPHYRIN IX CONTAINING FE × 7	ELECTRON MICROSCOPY cryo-EM buffer 20 mM HEPES (pH 7.5), 10 mM KCl, 1.5 mM MgCl2, 1 mM EDTA, 1 mM DTT；pH 7.5；20 mM HEPES (pH 7.5), 10 mM KCl, 1.5 mM MgCl2, 1 mM EDTA, 1 mM DTT cryo-EM vitrification conditions Blot for 2.5 seconds before plunging；Cryogen ETHANE	Resolution 3.80 Å
3NBT Crystal structure of trimeric cytochrome c from horse heart Deposited 2010-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–105（104 aa） Chain E 2–105（104 aa） Chain F 2–105（104 aa）	Not recorded	HEC HEME C × 3 PG4 TETRAETHYLENE GLYCOL × 3 PEG DI(HYDROXYETHYL)ETHER × 2 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；30% PEG 200, 0.1M Tris-HCl, 0.2M ammonium phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.10 Å R-free 0.254
3NBT Crystal structure of trimeric cytochrome c from horse heart Deposited 2010-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 2–105（104 aa） Chain C 2–105（104 aa） Chain D 2–105（104 aa）	Not recorded	HEC HEME C × 3 PG4 TETRAETHYLENE GLYCOL × 3 PEG DI(HYDROXYETHYL)ETHER × 2 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；30% PEG 200, 0.1M Tris-HCl, 0.2M ammonium phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.10 Å R-free 0.254
3O1Y Electron transfer complexes: Experimental mapping of the redox-dependent cytochrome c electrostatic surface Deposited 2010-07-22	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 2–105（104 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 1 NO3 NITRATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；300 K；High concentration of NaNO3 and 10% Ditionite in the wells, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.75 Å R-free 0.248
3O1Y Electron transfer complexes: Experimental mapping of the redox-dependent cytochrome c electrostatic surface Deposited 2010-07-22	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 2–105（104 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 1 NO3 NITRATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；300 K；High concentration of NaNO3 and 10% Ditionite in the wells, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.75 Å R-free 0.248
3O1Y Electron transfer complexes: Experimental mapping of the redox-dependent cytochrome c electrostatic surface Deposited 2010-07-22	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 2–105（104 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 1 NO3 NITRATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；300 K；High concentration of NaNO3 and 10% Ditionite in the wells, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.75 Å R-free 0.248
3O20 Electron transfer complexes:experimental mapping of the Redox-dependent Cytochrome C electrostatic surface Deposited 2010-07-22	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 2–105（104 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 1 NO3 NITRATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；300 K；Excess of NaNO3 and 10% of Ditionite, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.90 Å R-free 0.276
3O20 Electron transfer complexes:experimental mapping of the Redox-dependent Cytochrome C electrostatic surface Deposited 2010-07-22	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 2–105（104 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 1 NO3 NITRATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；300 K；Excess of NaNO3 and 10% of Ditionite, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.90 Å R-free 0.276
3O20 Electron transfer complexes:experimental mapping of the Redox-dependent Cytochrome C electrostatic surface Deposited 2010-07-22	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 2–105（104 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 1 NO3 NITRATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；300 K；Excess of NaNO3 and 10% of Ditionite, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.90 Å R-free 0.276
3WC8 Dimeric horse cytochrome c obtained by refolding with desalting method Deposited 2013-05-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–105（104 aa）	Not recorded	HEC HEME C × 2 PO4 PHOSPHATE ION × 2 PG4 TETRAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；100mM Tris-HCl buffer, 200mM (NH4)2HPO4, 40%(v/v) PEG200, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.80 Å R-free 0.208
3WUI Dimeric horse cytochrome c formed by refolding from molten globule state Deposited 2014-04-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–105（104 aa）	Not recorded	HEC HEME C × 2 PG4 TETRAETHYLENE GLYCOL × 2 PO4 PHOSPHATE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；100mM Tris-HCl buffer, 200mM (NH4)2HPO4, 40%(v/v) PEG 200, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.80 Å R-free 0.227
4NFG K13R mutant of horse cytochrome c and yeast cytochrome c peroxidase complex Deposited 2013-10-31	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 2–105（104 aa）	Mutation：K13R	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 UNX UNKNOWN LIGAND × 1 HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；15% PEG 3350, 150 mM NaCl, 0.5 mM 1:1 ratio of horse cytochrome c and yeast cytochrome c peroxidase, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.11 Å R-free 0.236
4RSZ The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c Deposited 2014-11-12	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 2–105（104 aa）	Not recorded	HEC HEME C × 1 CPT Cisplatin × 1 NO3 NITRATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；A new crystal form of horse heart cytochrome c that co-crystallized with nitrate and sulphate ions has been obtained. Crystallization was prepared by using the hanging-drop vapour diffusion method in Linbro plates and a reservoir contained 3.5 M ammonium sulphate, 0.6 M sodium nitrate. The droplets consisted of 1 microliter protein (30 mg/mL in water) and 1 microliter of reservoir. They were equilibrated against a 500 microliters reservoir solution at 20 C. These conditions produced well shaped red crystals after 1 month. These crystals have been soaked for 24 h in a solution consisting of 0.005 M cisplatin in 2.0 M ammonium sulphate and 0.4 M sodium nitrate. To prepare this solution, Cisplatin was first dissolved in 5 mM sodium acetate buffer at pH 5.0. , VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.19 Å R-free 0.282
4RSZ The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c Deposited 2014-11-12	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 2–105（104 aa）	Not recorded	HEC HEME C × 1 CPT Cisplatin × 1 NO3 NITRATE ION × 3 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；A new crystal form of horse heart cytochrome c that co-crystallized with nitrate and sulphate ions has been obtained. Crystallization was prepared by using the hanging-drop vapour diffusion method in Linbro plates and a reservoir contained 3.5 M ammonium sulphate, 0.6 M sodium nitrate. The droplets consisted of 1 microliter protein (30 mg/mL in water) and 1 microliter of reservoir. They were equilibrated against a 500 microliters reservoir solution at 20 C. These conditions produced well shaped red crystals after 1 month. These crystals have been soaked for 24 h in a solution consisting of 0.005 M cisplatin in 2.0 M ammonium sulphate and 0.4 M sodium nitrate. To prepare this solution, Cisplatin was first dissolved in 5 mM sodium acetate buffer at pH 5.0. , VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.19 Å R-free 0.282
4RSZ The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c Deposited 2014-11-12	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 2–105（104 aa）	Not recorded	HEC HEME C × 1 NO3 NITRATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；A new crystal form of horse heart cytochrome c that co-crystallized with nitrate and sulphate ions has been obtained. Crystallization was prepared by using the hanging-drop vapour diffusion method in Linbro plates and a reservoir contained 3.5 M ammonium sulphate, 0.6 M sodium nitrate. The droplets consisted of 1 microliter protein (30 mg/mL in water) and 1 microliter of reservoir. They were equilibrated against a 500 microliters reservoir solution at 20 C. These conditions produced well shaped red crystals after 1 month. These crystals have been soaked for 24 h in a solution consisting of 0.005 M cisplatin in 2.0 M ammonium sulphate and 0.4 M sodium nitrate. To prepare this solution, Cisplatin was first dissolved in 5 mM sodium acetate buffer at pH 5.0. , VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.19 Å R-free 0.282
4RSZ The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c Deposited 2014-11-12	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 2–105（104 aa）	Not recorded	HEC HEME C × 1 CPT Cisplatin × 1 NO3 NITRATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；A new crystal form of horse heart cytochrome c that co-crystallized with nitrate and sulphate ions has been obtained. Crystallization was prepared by using the hanging-drop vapour diffusion method in Linbro plates and a reservoir contained 3.5 M ammonium sulphate, 0.6 M sodium nitrate. The droplets consisted of 1 microliter protein (30 mg/mL in water) and 1 microliter of reservoir. They were equilibrated against a 500 microliters reservoir solution at 20 C. These conditions produced well shaped red crystals after 1 month. These crystals have been soaked for 24 h in a solution consisting of 0.005 M cisplatin in 2.0 M ammonium sulphate and 0.4 M sodium nitrate. To prepare this solution, Cisplatin was first dissolved in 5 mM sodium acetate buffer at pH 5.0. , VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.19 Å R-free 0.282
4RSZ The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c Deposited 2014-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 2–105（104 aa）	Not recorded	HEC HEME C × 1 CPT Cisplatin × 1 NO3 NITRATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；A new crystal form of horse heart cytochrome c that co-crystallized with nitrate and sulphate ions has been obtained. Crystallization was prepared by using the hanging-drop vapour diffusion method in Linbro plates and a reservoir contained 3.5 M ammonium sulphate, 0.6 M sodium nitrate. The droplets consisted of 1 microliter protein (30 mg/mL in water) and 1 microliter of reservoir. They were equilibrated against a 500 microliters reservoir solution at 20 C. These conditions produced well shaped red crystals after 1 month. These crystals have been soaked for 24 h in a solution consisting of 0.005 M cisplatin in 2.0 M ammonium sulphate and 0.4 M sodium nitrate. To prepare this solution, Cisplatin was first dissolved in 5 mM sodium acetate buffer at pH 5.0. , VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.19 Å R-free 0.282
4RSZ The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c Deposited 2014-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 2–105（104 aa）	Not recorded	HEC HEME C × 1 CPT Cisplatin × 1 NO3 NITRATE ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；A new crystal form of horse heart cytochrome c that co-crystallized with nitrate and sulphate ions has been obtained. Crystallization was prepared by using the hanging-drop vapour diffusion method in Linbro plates and a reservoir contained 3.5 M ammonium sulphate, 0.6 M sodium nitrate. The droplets consisted of 1 microliter protein (30 mg/mL in water) and 1 microliter of reservoir. They were equilibrated against a 500 microliters reservoir solution at 20 C. These conditions produced well shaped red crystals after 1 month. These crystals have been soaked for 24 h in a solution consisting of 0.005 M cisplatin in 2.0 M ammonium sulphate and 0.4 M sodium nitrate. To prepare this solution, Cisplatin was first dissolved in 5 mM sodium acetate buffer at pH 5.0. , VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.19 Å R-free 0.282
4RSZ The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c Deposited 2014-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–105（104 aa） Chain B 2–105（104 aa） Chain C 2–105（104 aa） Chain D 2–105（104 aa） Chain E 2–105（104 aa） Chain F 2–105（104 aa）	Not recorded	HEC HEME C × 6 CPT Cisplatin × 5 NO3 NITRATE ION × 16 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；A new crystal form of horse heart cytochrome c that co-crystallized with nitrate and sulphate ions has been obtained. Crystallization was prepared by using the hanging-drop vapour diffusion method in Linbro plates and a reservoir contained 3.5 M ammonium sulphate, 0.6 M sodium nitrate. The droplets consisted of 1 microliter protein (30 mg/mL in water) and 1 microliter of reservoir. They were equilibrated against a 500 microliters reservoir solution at 20 C. These conditions produced well shaped red crystals after 1 month. These crystals have been soaked for 24 h in a solution consisting of 0.005 M cisplatin in 2.0 M ammonium sulphate and 0.4 M sodium nitrate. To prepare this solution, Cisplatin was first dissolved in 5 mM sodium acetate buffer at pH 5.0. , VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.19 Å R-free 0.282
5IY5 Electron transfer complex of cytochrome c and cytochrome c oxidase at 2.0 angstrom resolution Deposited 2016-03-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain 1 2–105（104 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 HEA HEME-A × 2 PER PEROXIDE ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 TGL TRISTEAROYLGLYCEROL × 3 CUA DINUCLEAR COPPER ION × 1 EDO 1,2-ETHANEDIOL × 6 CHD CHOLIC ACID × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 1 CDL CARDIOLIPIN × 2 UNL UNKNOWN LIGAND × 5 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 8；277 K；15mM sodium phosphate, pH 8.0, 0.7% fluorinated octylmaltoside, 0.2% decylmaltoside, 3% ethylene glycol, 5% PEG 4000	Resolution 2.00 Å R-free 0.207
5IY5 Electron transfer complex of cytochrome c and cytochrome c oxidase at 2.0 angstrom resolution Deposited 2016-03-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain 2 2–105（104 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 HEA HEME-A × 2 PER PEROXIDE ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 3 TGL TRISTEAROYLGLYCEROL × 2 CUA DINUCLEAR COPPER ION × 1 EDO 1,2-ETHANEDIOL × 3 CHD CHOLIC ACID × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 1 CDL CARDIOLIPIN × 2 UNL UNKNOWN LIGAND × 10 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 8；277 K；15mM sodium phosphate, pH 8.0, 0.7% fluorinated octylmaltoside, 0.2% decylmaltoside, 3% ethylene glycol, 5% PEG 4000	Resolution 2.00 Å R-free 0.207
5WVE Apaf-1-Caspase-9 holoenzyme Deposited 2016-12-24	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 × 25 PDB declaration: 25-meric	Chain B 1–105（105 aa） Chain D 1–105（105 aa） Chain F 1–105（105 aa） Chain H 1–105（105 aa） Chain J 1–105（105 aa） Chain L 1–105（105 aa） Chain N 1–105（105 aa）	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 7 HEM PROTOPORPHYRIN IX CONTAINING FE × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
5ZKV Solution structure of molten globule state of L94G mutant of horse cytochrome-c Deposited 2018-03-26	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 2–105（104 aa）	Mutation：L94G	HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.03 M cacodylate buffer containing 0.1 M NaCl；Pressure 1 NMR sample composition 2 mM [U-99% 13C; U-99% 15N] Molten globule of L94G mutant of horse cytochrome-c, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6K9I High-resolution three-dimensional structure of horse heart cytochrome C at room temperature Deposited 2019-06-16	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 2–105（104 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；1.0-1.5M sodium chloride, 2.7-3.2M ammonium sulfate, 0.1M sodium phosphate	Resolution 1.80 Å R-free 0.199
6K9J 0.98 A three-dimensional structure of horse heart cytochrome C at 110K Deposited 2019-06-16	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 2–105（104 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；1.0-1.5M sodium chloride, 2.7-3.2M ammonium sulfate, 0.1M sodium phosphate	Resolution 0.98 Å R-free 0.153
6SUV Horse cytochrome c complexed by octa-anionic calixarene Deposited 2019-09-16	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 AaA 2–105（104 aa）	Not recorded	ACE ACETYL GROUP × 1 HEC HEME C × 1 LVQ octa-anionic calixarene × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；56% PEG 3350, 0.05 M sodium cacodylate pH 5.5 and 0.0017 M gadolinium chloride	Resolution 2.50 Å R-free 0.237
6SUV Horse cytochrome c complexed by octa-anionic calixarene Deposited 2019-09-16	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 BaB 2–105（104 aa）	Not recorded	ACE ACETYL GROUP × 1 HEC HEME C × 1 LVQ octa-anionic calixarene × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；56% PEG 3350, 0.05 M sodium cacodylate pH 5.5 and 0.0017 M gadolinium chloride	Resolution 2.50 Å R-free 0.237
6SUV Horse cytochrome c complexed by octa-anionic calixarene Deposited 2019-09-16	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 CaC 2–105（104 aa）	Not recorded	ACE ACETYL GROUP × 1 HEC HEME C × 1 LVQ octa-anionic calixarene × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；56% PEG 3350, 0.05 M sodium cacodylate pH 5.5 and 0.0017 M gadolinium chloride	Resolution 2.50 Å R-free 0.237
6SUV Horse cytochrome c complexed by octa-anionic calixarene Deposited 2019-09-16	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 DaD 2–105（104 aa）	Not recorded	ACE ACETYL GROUP × 1 HEC HEME C × 1 LVQ octa-anionic calixarene × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；56% PEG 3350, 0.05 M sodium cacodylate pH 5.5 and 0.0017 M gadolinium chloride	Resolution 2.50 Å R-free 0.237
6SUV Horse cytochrome c complexed by octa-anionic calixarene Deposited 2019-09-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain EaE 2–105（104 aa）	Not recorded	ACE ACETYL GROUP × 1 HEC HEME C × 1 LVQ octa-anionic calixarene × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；56% PEG 3350, 0.05 M sodium cacodylate pH 5.5 and 0.0017 M gadolinium chloride	Resolution 2.50 Å R-free 0.237
6SUV Horse cytochrome c complexed by octa-anionic calixarene Deposited 2019-09-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain FaF 2–105（104 aa）	Not recorded	ACE ACETYL GROUP × 1 HEC HEME C × 1 LVQ octa-anionic calixarene × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；56% PEG 3350, 0.05 M sodium cacodylate pH 5.5 and 0.0017 M gadolinium chloride	Resolution 2.50 Å R-free 0.237
6SUV Horse cytochrome c complexed by octa-anionic calixarene Deposited 2019-09-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain GaG 2–105（104 aa）	Not recorded	ACE ACETYL GROUP × 1 HEC HEME C × 1 LVQ octa-anionic calixarene × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；56% PEG 3350, 0.05 M sodium cacodylate pH 5.5 and 0.0017 M gadolinium chloride	Resolution 2.50 Å R-free 0.237
6SUV Horse cytochrome c complexed by octa-anionic calixarene Deposited 2019-09-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain HaH 2–105（104 aa）	Not recorded	ACE ACETYL GROUP × 1 HEC HEME C × 1 LVQ octa-anionic calixarene × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；56% PEG 3350, 0.05 M sodium cacodylate pH 5.5 and 0.0017 M gadolinium chloride	Resolution 2.50 Å R-free 0.237
8ZXR Crystal structure of Ssr1698 in complex with heme c Deposited 2024-06-14	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 12–22（11 aa）	Not recorded	NI NICKEL (II) ION × 1 CL CHLORIDE ION × 2 HEC HEME C × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Sodium acetate, Sodium formate, Glycerol	Resolution 1.60 Å R-free 0.218
8ZXR Crystal structure of Ssr1698 in complex with heme c Deposited 2024-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 12–22（11 aa）	Not recorded	NI NICKEL (II) ION × 6 CL CHLORIDE ION × 12 HEC HEME C × 6 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Sodium acetate, Sodium formate, Glycerol	Resolution 1.60 Å R-free 0.218
8ZXR Crystal structure of Ssr1698 in complex with heme c Deposited 2024-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 12–22（11 aa）	Not recorded	NI NICKEL (II) ION × 3 CL CHLORIDE ION × 6 HEC HEME C × 3 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Sodium acetate, Sodium formate, Glycerol	Resolution 1.60 Å R-free 0.218
8ZXR Crystal structure of Ssr1698 in complex with heme c Deposited 2024-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 12–22（11 aa）	Not recorded	NI NICKEL (II) ION × 2 CL CHLORIDE ION × 4 HEC HEME C × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Sodium acetate, Sodium formate, Glycerol	Resolution 1.60 Å R-free 0.218

32 other PDB entries and 56 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYC_HORSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–104； UniProt 2–105 Author chain B； PDBConstruct 1–104； UniProt 2–105 Author chain C； PDBConstruct 1–104； UniProt 2–105 Author chain D； PDBConstruct 1–104； UniProt 2–105

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3nbs
Deposition date deposition_date	2010-06-04
Structure title title	Crystal structure of dimeric cytochrome c from horse heart
Keywords keywords	cytochrome c, polymerization, domain swapping, Electron Transport; ELECTRON TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.07 Å
Radius of gyration Rg (electron density) rg_electron	26.18 Å
Forward intensity I(0) i0	39387400.00
Molecular weight molecular_weight	50107.0 kDa
Excluded volume excluded_volume	63389 Å³
Envelope volume envelope_volume	79321 Å³
Hydration-shell volume shell_volume	25619 Å³
Envelope diameter envelope_diameter	85.1 Å
Shell Rg shell_rg	33.28 Å
Envelope Rg envelope_rg	25.52 Å
Shape Rg shape_rg	26.17 Å
Total Rg total_rg	27.03 Å
Total atoms total_atoms	3514
Residues n_residues	416
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	79.8 Å
Rg (real space) rg_real	26.97 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	3.9390e+07
I(0) uncertainty (real space) i0_real_error	5.0760e+05
Rg (reciprocal space) rg_reciprocal	27.00 Å
I(0) (reciprocal space) i0_reciprocal	39390000.0000
Solution quality estimate total_estimate	0.9129
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	39.2 Å
Skewness Skewness skewness	0.090
Kurtosis Kurtosis kurtosis	-0.724
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13980000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.977; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.942

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Cytochrome c
Molecular weight formula_weight	11725.6 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3776

GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE

Entity 2 Entity 2 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	262

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3nbsa_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

Domain ID domain_id	d3nbsb_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

Domain ID domain_id	d3nbsc_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

Domain ID domain_id	d3nbsd_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

CATH v4.4 (4 domains)

Domain ID domain_id	3nbsA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	3nbsB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	3nbsC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	3nbsD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

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8. Citations (1)

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Unit-cell length a length_a	41.753 Å
Unit-cell length b length_b	56.305 Å
Unit-cell length c length_c	60.815 Å
Unit-cell angle α angle_alpha	66.28 °
Unit-cell angle β angle_beta	89.94 °
Unit-cell angle γ angle_gamma	73.66 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	19.580 Å
R factor r_factor	0.2150
R_work r_work	0.2150
R_free r_free	0.2730

fit	/app/data/saxs_computation/nb/3nbs/3nbs.fit
pddf	/app/data/pr_computation/nb/3nbs/3nbs.pr.out
profile	/app/data/saxs_computation/nb/3nbs/3nbs.dat