Solution structure of oxidized human cytochrome c
GDVEKGKKIF IMKCSQCHTV EKGGKHKTGP NLHGLFGRKT GQAPGYSYTA ANKNKGIIWG EDTLMEYLEN PKKYIPGTKM IFVGIKKKEE RADLIAYLKK ATNE
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | thioether | sing | 1:CYS14:SG | 2:HEC1:CAB |
2 | thioether | sing | 1:CYS17:SG | 2:HEC1:CAC |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 97.1 % (1216 of 1252) | 98.0 % (649 of 662) | 95.9 % (462 of 482) | 97.2 % (105 of 108) |
Backbone | 98.2 % (605 of 616) | 99.1 % (215 of 217) | 98.0 % (293 of 299) | 97.0 % (97 of 100) |
Sidechain | 96.4 % (701 of 727) | 97.5 % (434 of 445) | 94.5 % (259 of 274) | 100.0 % (8 of 8) |
Aromatic | 83.0 % (78 of 94) | 89.4 % (42 of 47) | 76.1 % (35 of 46) | 100.0 % (1 of 1) |
Methyl | 100.0 % (94 of 94) | 100.0 % (47 of 47) | 100.0 % (47 of 47) |
1. Cyt c
GDVEKGKKIF IMKCSQCHTV EKGGKHKTGP NLHGLFGRKT GQAPGYSYTA ANKNKGIIWG EDTLMEYLEN PKKYIPGTKM IFVGIKKKEE RADLIAYLKK ATNESolvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Agilent INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Agilent INOVA - 800 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Agilent INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Agilent INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Agilent INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Agilent INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Agilent INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Agilent INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Agilent INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Agilent INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Agilent INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Agilent INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Agilent INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Agilent INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Agilent INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Agilent INOVA - 800 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Agilent INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Agilent INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Agilent INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cyt c | [U-99% 13C; U-99% 15N] | protein | 0.5 ~ 1.0 mM |
2 | sodium phosphate | natural abundance | buffer | 50 mM |
3 | H2O | natural abundance | solvent | 95 % |
4 | D2O | [U-2H] | solvent | 5 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_25908_2n9j.nef |
Input source #2: Coordindates | 2n9j.cif |
Diamagnetism of the molecular assembly | False (excluding Oxygen atoms) |
Whether the assembly has a disulfide bond | None |
Whether the assembly has a other bond | True (see coodinates for details) |
Whether the assembly contains a cyclic polymer | None |
Overall data processing status | Warning |
Disulfide bonds
NoneOther bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
Ptnr_site_1 | Ptnr_site_2 | Redox_state_prediction_1 | Redox_state_prediction_2 | Distance (Ã…) |
---|---|---|---|---|
1:18:HIS:NE2 | 2:1:HEC:FE | unknown | unknown | n/a |
1:80:MET:SD | 2:1:HEC:FE | unknown | unknown | n/a |
1:14:CYS:SG | 2:1:HEC:CAB | unknown | unknown | n/a |
1:17:CYS:SG | 2:1:HEC:CAC | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 1 | HEC | HEME C | Assigned chemical shifts |
Sequence alignments
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKK |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKK ---- ATNE |||| ATNE
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 104 | 0 | 0 | 100.0 |
Content subtype: combined_25908_2n9j.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKK |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKK ---- ATNE |||| ATNE
- X | X
Comp_index_ID | Comp_ID | Atom_ID | CS value (ppm) |
---|---|---|---|
16 | GLN | CD | 180.294 |
31 | ASN | CG | 177.928 |
38 | ARG | HH11 | 6.729 |
38 | ARG | CZ | 184.485 |
40 | THR | HG1 | 3.995 |
42 | GLN | CD | 180.274 |
48 | TYR | HH | 8.774 |
49 | THR | HG1 | 9.569 |
52 | ASN | CG | 175.388 |
54 | ASN | CG | 176.952 |
63 | THR | HG1 | 4.381 |
70 | ASN | CG | 178.082 |
91 | ARG | CZ | 184.31 |
102 | THR | HG1 | 4.836 |
103 | ASN | CG | 177.745 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 662 | 646 | 97.6 |
13C chemical shifts | 482 | 456 | 94.6 |
15N chemical shifts | 110 | 105 | 95.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 217 | 214 | 98.6 |
13C chemical shifts | 208 | 199 | 95.7 |
15N chemical shifts | 100 | 95 | 95.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 445 | 432 | 97.1 |
13C chemical shifts | 274 | 257 | 93.8 |
15N chemical shifts | 10 | 10 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 50 | 49 | 98.0 |
13C chemical shifts | 50 | 49 | 98.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 47 | 40 | 85.1 |
13C chemical shifts | 46 | 33 | 71.7 |
15N chemical shifts | 1 | 1 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 22 | 12 | 54.5 |
13C chemical shifts | 34 | 0 | 0.0 |
15N chemical shifts | 4 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 22 | 12 | 54.5 |
13C chemical shifts | 34 | 0 | 0.0 |
15N chemical shifts | 4 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 6 | 6 | 100.0 |
13C chemical shifts | 6 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 16 | 0 | 0.0 |
15N chemical shifts | 4 | 0 | 0.0 |
Covalent bonds
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKK |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||| GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAP.YSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKK ---- ATNE |||| ATNE
Dihedral angle restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKK ||||||||||||||||| ||| ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GDVEKGKKIFIMKCSQC..VEK.GKHKTGPNLHGLFGRKT.QAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKK --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 ---- ATNE ||| ATN ---