1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Banci, L.
Bertini, I.
Liu, G.
Lu, J.
Reddig, T.
Tang, W.
Wu, Y.
Zhu, D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
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
C3 H5 N2 1
69.085
IMIDAZOLE
non-polymer
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
6
628
637
10.1007/s007750100240
11472026
Effects of extrinsic imidazole ligation on the molecular and electronic structure of cytochrome c
2001
10.2210/pdb1fi7/pdb
pdb_00001fi7
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
11725.598
CYTOCHROME C
1
nat
polymer
69.085
IMIDAZOLE
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
2000-08-23
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
1FI9 contains the ensemble of structures.
RCSB
Y
RCSB
2000-08-03
REL
IMD
IMIDAZOLE
HEC
HEME C
1
2D NOESY
2D NOESY
DQF-COSY
DQF-COSY
TOCSY
TOCSY
5.7
1
atm
313
K
OTHER REFINEMENT REMARKS: DYNAMICS SIMULATED ANNEALING,RESTRAINED ENERGY MINIMIZATION; PSEUDOCONTACT SHIFTS WERE USED IN THE CALCULATION AND IN THE MINIMIZATION AS FURTHER NON-CLASSICAL CONSTRAINTS
AMBER
minimized average structure
6mM cytochrome c, 1.2M Imidazole
H2O
6mM cytochrome c, 1.2M Imidazole
D2O
Wuthrich et al
structure solution
DYANA
5.0
Banci et al
structure solution
PSEUDODYANA
5.0
PEARLMAN, CASE, CALDWELL, ROSS, CHEATHAM, FERGUSON, SEIBEL, SINGH, WEINER, KOLLMAN
refinement
Amber
5.0
BANCI, BERTINI, GORI SAVELLINI, ROMAGNOLI, TURANO, CREMONINI, LUCHINAT,GARY
refinement
PSEUDOREM
5.0
600
Bruker
AMX
IMD
105
2
IMD
IMD
105
A
HES
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
CYM
14
n
14
CYS
14
A
ALA
15
n
15
ALA
15
A
GLN
16
n
16
GLN
16
A
CYM
17
n
17
CYS
17
A
HES
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
HID
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
HID
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
93.1
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
89.9
A
HEC
110
C
NA
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
HEC
110
C
NB
HEC
1_555
89.7
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
86.9
A
HEC
110
C
NA
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
HEC
110
C
NC
HEC
1_555
179.5
A
HEC
110
C
NB
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
HEC
110
C
NC
HEC
1_555
89.8
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
85.5
A
HEC
110
C
NA
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
HEC
110
C
ND
HEC
1_555
89.9
A
HEC
110
C
NB
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
HEC
110
C
ND
HEC
1_555
175.4
A
HEC
110
C
NC
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
HEC
110
C
ND
HEC
1_555
90.6
A
HIS
18
A
NE2
HIS
18
1_555
A
HEC
110
C
FE
HEC
1_555
A
IMD
105
B
N3
IMD
1_555
172.2
A
HEC
110
C
NA
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
IMD
105
B
N3
IMD
1_555
93.4
A
HEC
110
C
NB
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
IMD
105
B
N3
IMD
1_555
94.3
A
HEC
110
C
NC
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
IMD
105
B
N3
IMD
1_555
86.6
A
HEC
110
C
ND
HEC
1_555
A
HEC
110
C
FE
HEC
1_555
A
IMD
105
B
N3
IMD
1_555
90.3
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
TYR
74
0.063
SIDE CHAIN
1
-4.75
0.60
121.00
116.25
A
A
A
CB
CG
CD2
TYR
TYR
TYR
48
48
48
N
1
3.67
0.60
121.00
124.67
A
A
A
CB
CG
CD1
TYR
TYR
TYR
48
48
48
N
1
A
ALA
15
-0.70
-71.96
1
A
CYS
17
-164.88
-44.09
1
A
LYS
27
37.22
-126.37
1
A
ASN
31
-59.50
102.64
1
A
GLN
42
-149.06
58.05
1
A
ASP
50
-62.73
14.50
1
A
LYS
60
-155.67
-11.32
1
A
GLU
61
134.91
-52.07
1
A
ASN
70
-152.30
56.68
1
A
LYS
72
-83.96
48.03
1
A
LYS
73
-145.40
-49.10
1
A
ILE
75
-162.08
117.75
1
A
THR
78
-127.59
-67.77
1
A
LYS
79
-174.79
-31.50
1
A
MET
80
55.86
83.81
1
A
ILE
81
-98.98
-118.18
1
A
ILE
85
-54.68
-81.49
1
A
LYS
86
-148.70
-50.69
1
A
LYS
87
-166.40
-153.20
1
A
THR
89
-49.51
-70.54
minimized average
Solution structure of the imidazole complex of cytochrome 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
ALA
51
A
ALA
51
HELX_P
A
GLY
56
A
GLY
56
1
2
6
A
GLU
61
A
GLU
61
HELX_P
A
ASN
70
A
ASN
70
1
3
10
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
1.824
none
A
CYS
14
A
SG
CYS
14
1_555
A
HEC
110
C
CAB
HEC
1_555
covale
1.806
none
A
CYS
17
A
SG
CYS
17
1_555
A
HEC
110
C
CAC
HEC
1_555
metalc
1.936
A
HIS
18
A
NE2
HIS
18
1_555
A
HEC
110
C
FE
HEC
1_555
metalc
1.968
A
IMD
105
B
N3
IMD
1_555
A
HEC
110
C
FE
HEC
1_555
ELECTRON TRANSPORT
cytochrome c, solution structure, ELECTRON TRANSPORT
CYC_HORSE
UNP
1
1
P00004
GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKM
IFAGIKKKTEREDLIAYLKKATNE
1
104
1FI7
1
104
P00004
A
1
1
104
BINDING SITE FOR RESIDUE IMD A 105
A
IMD
105
Software
3
BINDING SITE FOR RESIDUE HEC A 110
A
HEC
110
Software
16
A
TYR
67
A
TYR
67
3
1_555
A
LYS
79
A
LYS
79
3
1_555
A
HEC
110
C
HEC
3
1_555
A
CYS
14
A
CYS
14
16
1_555
A
CYS
17
A
CYS
17
16
1_555
A
HIS
18
A
HIS
18
16
1_555
A
THR
28
A
THR
28
16
1_555
A
GLY
29
A
GLY
29
16
1_555
A
PRO
30
A
PRO
30
16
1_555
A
LEU
32
A
LEU
32
16
1_555
A
THR
40
A
THR
40
16
1_555
A
THR
49
A
THR
49
16
1_555
A
ASN
52
A
ASN
52
16
1_555
A
TRP
59
A
TRP
59
16
1_555
A
LEU
64
A
LEU
64
16
1_555
A
LEU
68
A
LEU
68
16
1_555
A
THR
78
A
THR
78
16
1_555
A
LYS
79
A
LYS
79
16
1_555
A
IMD
105
B
IMD
16
1_555
1
P 1