1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Yao, Y.
Qian, C.
Ye, K.
Wang, J.
Tang, W.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C N -1
26.017
CYANIDE ION
non-polymer
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C34 H34 Fe N4 O4
618.503
HEME C
non-polymer
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
GW
J.Biol.Inorg.Chem.
JJBCFA
2154
0949-8257
7
539
547
10.1007/s00775-001-0334-y
11941512
Solution structure of cyanoferricytochrome c: ligand-controlled conformational flexibility and electronic structure of the heme moiety.
2002
10.2210/pdb1i5t/pdb
pdb_00001i5t
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
11725.598
CYTOCHROME C
1
nat
polymer
26.017
CYANIDE ION
1
syn
non-polymer
618.503
HEME C
1
syn
non-polymer
no
no
GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKM
IFAGIKKKTEREDLIAYLKKATNE
GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKM
IFAGIKKKTEREDLIAYLKKATNE
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
horse
Equus
sample
9796
Equus caballus
HEART
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_conn_type
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2001-03-21
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.conn_type_id
_struct_conn.id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn_type.id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
1AKK contains solution structure of the native oxidized horse heart cytochrome c
1I5U contains SOLUTION STRUCTURE OF CYTOCHROME B5 TRIPLE MUTANT
(E48A/E56A/D60A)
RCSB
Y
PDBJ
2001-02-28
REL
REL
CYN
CYANIDE ION
HEC
HEME C
all calculated structures submitted
35
1
7.0
303
K
torsion angle dynamics
minimized average structure
5mM cytochrome c,50mM potassium cyanide
90% H2O/10% D2O
5mM cytochrome c, 50mM potassium cyanide
D2O
processing
XwinNMR
2.6
structure solution
DYANA
1.5
refinement
Amber
5.0
600
Bruker
DMX
500
Bruker
DRX
CYA
105
2
CYN
CYN
105
A
HIS
18
3
HEC
HEC
110
A
GLY
1
n
1
GLY
1
A
ASP
2
n
2
ASP
2
A
VAL
3
n
3
VAL
3
A
GLU
4
n
4
GLU
4
A
LYS
5
n
5
LYS
5
A
GLY
6
n
6
GLY
6
A
LYS
7
n
7
LYS
7
A
LYS
8
n
8
LYS
8
A
ILE
9
n
9
ILE
9
A
PHE
10
n
10
PHE
10
A
VAL
11
n
11
VAL
11
A
GLN
12
n
12
GLN
12
A
LYS
13
n
13
LYS
13
A
CYS
14
n
14
CYS
14
A
ALA
15
n
15
ALA
15
A
GLN
16
n
16
GLN
16
A
CYS
17
n
17
CYS
17
A
HIS
18
n
18
HIS
18
A
THR
19
n
19
THR
19
A
VAL
20
n
20
VAL
20
A
GLU
21
n
21
GLU
21
A
LYS
22
n
22
LYS
22
A
GLY
23
n
23
GLY
23
A
GLY
24
n
24
GLY
24
A
LYS
25
n
25
LYS
25
A
HIS
26
n
26
HIS
26
A
LYS
27
n
27
LYS
27
A
THR
28
n
28
THR
28
A
GLY
29
n
29
GLY
29
A
PRO
30
n
30
PRO
30
A
ASN
31
n
31
ASN
31
A
LEU
32
n
32
LEU
32
A
HIS
33
n
33
HIS
33
A
GLY
34
n
34
GLY
34
A
LEU
35
n
35
LEU
35
A
PHE
36
n
36
PHE
36
A
GLY
37
n
37
GLY
37
A
ARG
38
n
38
ARG
38
A
LYS
39
n
39
LYS
39
A
THR
40
n
40
THR
40
A
GLY
41
n
41
GLY
41
A
GLN
42
n
42
GLN
42
A
ALA
43
n
43
ALA
43
A
PRO
44
n
44
PRO
44
A
GLY
45
n
45
GLY
45
A
PHE
46
n
46
PHE
46
A
THR
47
n
47
THR
47
A
TYR
48
n
48
TYR
48
A
THR
49
n
49
THR
49
A
ASP
50
n
50
ASP
50
A
ALA
51
n
51
ALA
51
A
ASN
52
n
52
ASN
52
A
LYS
53
n
53
LYS
53
A
ASN
54
n
54
ASN
54
A
LYS
55
n
55
LYS
55
A
GLY
56
n
56
GLY
56
A
ILE
57
n
57
ILE
57
A
THR
58
n
58
THR
58
A
TRP
59
n
59
TRP
59
A
LYS
60
n
60
LYS
60
A
GLU
61
n
61
GLU
61
A
GLU
62
n
62
GLU
62
A
THR
63
n
63
THR
63
A
LEU
64
n
64
LEU
64
A
MET
65
n
65
MET
65
A
GLU
66
n
66
GLU
66
A
TYR
67
n
67
TYR
67
A
LEU
68
n
68
LEU
68
A
GLU
69
n
69
GLU
69
A
ASN
70
n
70
ASN
70
A
PRO
71
n
71
PRO
71
A
LYS
72
n
72
LYS
72
A
LYS
73
n
73
LYS
73
A
TYR
74
n
74
TYR
74
A
ILE
75
n
75
ILE
75
A
PRO
76
n
76
PRO
76
A
GLY
77
n
77
GLY
77
A
THR
78
n
78
THR
78
A
LYS
79
n
79
LYS
79
A
MET
80
n
80
MET
80
A
ILE
81
n
81
ILE
81
A
PHE
82
n
82
PHE
82
A
ALA
83
n
83
ALA
83
A
GLY
84
n
84
GLY
84
A
ILE
85
n
85
ILE
85
A
LYS
86
n
86
LYS
86
A
LYS
87
n
87
LYS
87
A
LYS
88
n
88
LYS
88
A
THR
89
n
89
THR
89
A
GLU
90
n
90
GLU
90
A
ARG
91
n
91
ARG
91
A
GLU
92
n
92
GLU
92
A
ASP
93
n
93
ASP
93
A
LEU
94
n
94
LEU
94
A
ILE
95
n
95
ILE
95
A
ALA
96
n
96
ALA
96
A
TYR
97
n
97
TYR
97
A
LEU
98
n
98
LEU
98
A
LYS
99
n
99
LYS
99
A
LYS
100
n
100
LYS
100
A
ALA
101
n
101
ALA
101
A
THR
102
n
102
THR
102
A
ASN
103
n
103
ASN
103
A
GLU
104
n
104
GLU
104
A
author_defined_assembly
1
monomeric
A
HIS
18
A
NE2
HIS
18
1_555
A
HEC
110
C
FE
HEC
1_555
A
HEC
110
C
NA
HEC
1_555
95.8
A
HIS
18
A
NE2
HIS
18
1_555
A
HEC
110
C
FE
HEC
1_555
A
HEC
110
C
NB
HEC
1_555
93.0
A
HEC
110
C
NA
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
HEC
110
C
NB
HEC
1_555
91.1
A
HIS
18
A
NE2
HIS
18
1_555
A
HEC
110
C
FE
HEC
1_555
A
HEC
110
C
NC
HEC
1_555
89.9
A
HEC
110
C
NA
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
HEC
110
C
NC
HEC
1_555
173.6
A
HEC
110
C
NB
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
HEC
110
C
NC
HEC
1_555
91.4
A
HIS
18
A
NE2
HIS
18
1_555
A
HEC
110
C
FE
HEC
1_555
A
HEC
110
C
ND
HEC
1_555
91.0
A
HEC
110
C
NA
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
HEC
110
C
ND
HEC
1_555
88.5
A
HEC
110
C
NB
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
HEC
110
C
ND
HEC
1_555
176.0
A
HEC
110
C
NC
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
HEC
110
C
ND
HEC
1_555
88.6
A
HIS
18
A
NE2
HIS
18
1_555
A
HEC
110
C
FE
HEC
1_555
A
CYN
105
B
C
CYN
1_555
176.8
A
HEC
110
C
NA
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
CYN
105
B
C
CYN
1_555
87.0
A
HEC
110
C
NB
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
CYN
105
B
C
CYN
1_555
85.3
A
HEC
110
C
NC
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
CYN
105
B
C
CYN
1_555
87.4
A
HEC
110
C
ND
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
CYN
105
B
C
CYN
1_555
90.7
A
HIS
18
A
NE2
HIS
18
1_555
A
HEC
110
C
FE
HEC
1_555
A
CYN
105
B
N
CYN
1_555
175.6
A
HEC
110
C
NA
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
CYN
105
B
N
CYN
1_555
87.7
A
HEC
110
C
NB
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
CYN
105
B
N
CYN
1_555
84.4
A
HEC
110
C
NC
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
CYN
105
B
N
CYN
1_555
86.7
A
HEC
110
C
ND
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
CYN
105
B
N
CYN
1_555
91.6
A
CYN
105
B
C
CYN
1_555
A
HEC
110
C
FE
HEC
1_555
A
CYN
105
B
N
CYN
1_555
1.2
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1
A
A
THR
LYS
78
79
149.32
1
A
HIS
18
0.085
SIDE CHAIN
1
A
TYR
48
0.078
SIDE CHAIN
1
A
TYR
67
0.075
SIDE CHAIN
1
A
TYR
74
0.079
SIDE CHAIN
1
A
ARG
91
0.145
SIDE CHAIN
1
A
LYS
13
-142.57
28.02
1
A
CYS
14
-133.92
-49.80
1
A
LYS
27
-107.21
-146.19
1
A
HIS
33
13.86
84.69
1
A
LYS
60
-126.02
-94.55
1
A
GLU
61
-147.76
-52.94
1
A
MET
80
-66.37
-84.25
1
A
ILE
81
-150.11
-50.09
minimized average
SOLUTION STRUCTURE OF CYANOFERRICYTOCHROME C
1
N
N
2
N
N
3
N
N
A
ASP
2
A
ASP
2
HELX_P
A
CYS
14
A
CYS
14
1
1
13
A
THR
49
A
THR
49
HELX_P
A
GLY
56
A
GLY
56
1
2
8
A
GLU
61
A
GLU
61
HELX_P
A
LEU
68
A
LEU
68
1
3
8
A
ASN
70
A
ASN
70
HELX_P
A
ILE
75
A
ILE
75
1
4
6
A
LYS
87
A
LYS
87
HELX_P
A
GLU
104
A
GLU
104
1
5
18
covale
1.841
none
A
CYS
14
A
SG
CYS
14
1_555
A
HEC
110
C
CAB
HEC
1_555
covale
1.833
none
A
CYS
17
A
SG
CYS
17
1_555
A
HEC
110
C
CAC
HEC
1_555
metalc
1.958
A
HIS
18
A
NE2
HIS
18
1_555
A
HEC
110
C
FE
HEC
1_555
metalc
1.837
A
CYN
105
B
C
CYN
1_555
A
HEC
110
C
FE
HEC
1_555
metalc
3.094
A
CYN
105
B
N
CYN
1_555
A
HEC
110
C
FE
HEC
1_555
ELECTRON TRANSPORT
cytochrome c, cyanide, conformational transition, ELECTRON TRANSPORT
A
MET
80
A
MET
80
1
A
ILE
81
A
ILE
81
-13.23
CYC_HORSE
UNP
1
P00004
1
104
1I5T
1
104
P00004
A
1
1
104
BINDING SITE FOR RESIDUE CYN A 105
A
CYN
105
Software
2
BINDING SITE FOR RESIDUE HEC A 110
A
HEC
110
Software
11
A
TYR
67
A
TYR
67
2
1_555
A
HEC
110
C
HEC
2
1_555
A
LYS
13
A
LYS
13
11
1_555
A
CYS
14
A
CYS
14
11
1_555
A
GLN
16
A
GLN
16
11
1_555
A
CYS
17
A
CYS
17
11
1_555
A
HIS
18
A
HIS
18
11
1_555
A
THR
28
A
THR
28
11
1_555
A
PRO
30
A
PRO
30
11
1_555
A
TRP
59
A
TRP
59
11
1_555
A
TYR
67
A
TYR
67
11
1_555
A
LEU
68
A
LEU
68
11
1_555
A
CYN
105
B
CYN
11
1_555