.022841
.013188
0.000000
0.000000
.026375
0.000000
0.000000
0.000000
.009087
0.00000
0.00000
0.00000
RESIDUE LYS 80 AND TML 2 FORM EPSILON-N-TRIMETHYLLYSINE. SEE REMARK 4 ABOVE.
RESIDUE LYS 94 AND TML 3 FORM EPSILON-N-TRIMETHYLLYSINE. SEE REMARK 4 ABOVE.
Ochi, H.
Hata, Y.
Tanaka, N.
Kakudo, M.
Sakurai, T.
Aihara, S.
Morita, Y.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
43.780
43.780
110.050
C2 H4 O
44.053
ACETYL GROUP
non-polymer
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
H2 O
18.015
WATER
non-polymer
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
C9 H21 N2 O2 1
189.275
n
N-TRIMETHYLLYSINE
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
C3 H7 N O3
105.093
y
SERINE
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
166
407
418
10.1016/S0022-2836(83)80092-8
6304326
Structure of rice ferricytochrome c at 2.0 A resolution.
1983
JA
J.Biochem.(Tokyo)
JOBIAO
0418
0021-924X
87
249
Amino Acid Sequence of Cytochrome C from Rice
1980
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
71
807
A Preliminary Crystallographic Investigation of Rice Cytochrome C
1972
JA
Agric.Biol.Chem.
ABCHA6
0137
0002-1369
32
441
Studies on Respiratory Enzymes in Rice Kernel. Part I. Isolation and Purification of Cytochrome C and Peroxidase 556 from Rice Embryo
1968
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
x-ray
1
1.0
12267.986
CYTOCHROME C
1
man
polymer
618.503
HEME C
1
syn
non-polymer
18.015
water
46
nat
water
no
yes
(ACE)ASFSEAPPGNPKAGEKIFKTKCAQCHTVDKGAGHKQGPNLNGLFGRQSGTTPGYSYSTADKNMAVIWEENTLYDY
LLNP(M3L)KYIPGTKMVFPGL(M3L)KPQERADLISYLKEATS
XASFSEAPPGNPKAGEKIFKTKCAQCHTVDKGAGHKQGPNLNGLFGRQSGTTPGYSYSTADKNMAVIWEENTLYDYLLNP
KKYIPGTKMVFPGLKKPQERADLISYLKEATS
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
n
n
n
n
n
n
n
n
rice
Oryza
sample
4530
Oryza sativa
2.50
50.74
pdbx_database_status
struct_conf
struct_conf_type
atom_site
chem_comp
entity
pdbx_entity_nonpoly
pdbx_nonpoly_scheme
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Version format compliance
Derived calculations
Other
Atomic model
Data collection
Database references
Derived calculations
Non-polymer description
Structure summary
1
0
1983-04-21
1
1
2008-03-21
1
2
2011-07-13
1
3
2017-11-29
2
0
2021-03-03
_pdbx_database_status.process_site
_atom_site.B_iso_or_equiv
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.type_symbol
_chem_comp.formula
_chem_comp.formula_weight
_chem_comp.id
_chem_comp.name
_chem_comp.pdbx_synonyms
_entity.formula_weight
_entity.pdbx_description
_pdbx_entity_nonpoly.comp_id
_pdbx_entity_nonpoly.name
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr2_auth_comp_id
_pdbx_struct_conn_angle.ptnr2_label_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_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_ref_seq_dif.details
_struct_site.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
BNL
1983-03-14
REL
REL
HEC
HEME C
HOH
water
HEM
1
2
HEC
HEC
112
A
HOH
4
3
HOH
HOH
113
A
HOH
5
3
HOH
HOH
114
A
HOH
6
3
HOH
HOH
115
A
HOH
7
3
HOH
HOH
116
A
HOH
8
3
HOH
HOH
117
A
HOH
9
3
HOH
HOH
118
A
HOH
10
3
HOH
HOH
119
A
HOH
11
3
HOH
HOH
120
A
HOH
12
3
HOH
HOH
121
A
HOH
13
3
HOH
HOH
122
A
HOH
14
3
HOH
HOH
123
A
HOH
15
3
HOH
HOH
124
A
HOH
16
3
HOH
HOH
125
A
HOH
17
3
HOH
HOH
126
A
HOH
18
3
HOH
HOH
127
A
HOH
19
3
HOH
HOH
128
A
HOH
20
3
HOH
HOH
129
A
HOH
21
3
HOH
HOH
130
A
HOH
22
3
HOH
HOH
131
A
HOH
23
3
HOH
HOH
132
A
HOH
24
3
HOH
HOH
133
A
HOH
25
3
HOH
HOH
134
A
HOH
26
3
HOH
HOH
135
A
HOH
27
3
HOH
HOH
136
A
HOH
28
3
HOH
HOH
137
A
HOH
29
3
HOH
HOH
138
A
HOH
30
3
HOH
HOH
139
A
HOH
31
3
HOH
HOH
140
A
HOH
32
3
HOH
HOH
141
A
HOH
33
3
HOH
HOH
142
A
HOH
34
3
HOH
HOH
143
A
HOH
35
3
HOH
HOH
144
A
HOH
36
3
HOH
HOH
145
A
HOH
37
3
HOH
HOH
146
A
HOH
38
3
HOH
HOH
147
A
HOH
39
3
HOH
HOH
148
A
HOH
40
3
HOH
HOH
149
A
HOH
41
3
HOH
HOH
150
A
HOH
42
3
HOH
HOH
151
A
HOH
43
3
HOH
HOH
152
A
HOH
44
3
HOH
HOH
153
A
HOH
45
3
HOH
HOH
154
A
HOH
46
3
HOH
HOH
155
A
HOH
47
3
HOH
HOH
156
A
HOH
48
3
HOH
HOH
157
A
HOH
49
3
HOH
HOH
158
A
ACE
0
n
1
ACE
0
A
ALA
1
n
2
ALA
1
A
SER
2
n
3
SER
2
A
PHE
3
n
4
PHE
3
A
SER
4
n
5
SER
4
A
GLU
5
n
6
GLU
5
A
ALA
6
n
7
ALA
6
A
PRO
7
n
8
PRO
7
A
PRO
8
n
9
PRO
8
A
GLY
9
n
10
GLY
9
A
ASN
10
n
11
ASN
10
A
PRO
11
n
12
PRO
11
A
LYS
12
n
13
LYS
12
A
ALA
13
n
14
ALA
13
A
GLY
14
n
15
GLY
14
A
GLU
15
n
16
GLU
15
A
LYS
16
n
17
LYS
16
A
ILE
17
n
18
ILE
17
A
PHE
18
n
19
PHE
18
A
LYS
19
n
20
LYS
19
A
THR
20
n
21
THR
20
A
LYS
21
n
22
LYS
21
A
CYS
22
n
23
CYS
22
A
ALA
23
n
24
ALA
23
A
GLN
24
n
25
GLN
24
A
CYS
25
n
26
CYS
25
A
HIS
26
n
27
HIS
26
A
THR
27
n
28
THR
27
A
VAL
28
n
29
VAL
28
A
ASP
29
n
30
ASP
29
A
LYS
30
n
31
LYS
30
A
GLY
31
n
32
GLY
31
A
ALA
32
n
33
ALA
32
A
GLY
33
n
34
GLY
33
A
HIS
34
n
35
HIS
34
A
LYS
35
n
36
LYS
35
A
GLN
36
n
37
GLN
36
A
GLY
37
n
38
GLY
37
A
PRO
38
n
39
PRO
38
A
ASN
39
n
40
ASN
39
A
LEU
40
n
41
LEU
40
A
ASN
41
n
42
ASN
41
A
GLY
42
n
43
GLY
42
A
LEU
43
n
44
LEU
43
A
PHE
44
n
45
PHE
44
A
GLY
45
n
46
GLY
45
A
ARG
46
n
47
ARG
46
A
GLN
47
n
48
GLN
47
A
SER
48
n
49
SER
48
A
GLY
49
n
50
GLY
49
A
THR
50
n
51
THR
50
A
THR
51
n
52
THR
51
A
PRO
52
n
53
PRO
52
A
GLY
53
n
54
GLY
53
A
TYR
54
n
55
TYR
54
A
SER
55
n
56
SER
55
A
TYR
56
n
57
TYR
56
A
SER
57
n
58
SER
57
A
THR
58
n
59
THR
58
A
ALA
59
n
60
ALA
59
A
ASP
60
n
61
ASP
60
A
LYS
61
n
62
LYS
61
A
ASN
62
n
63
ASN
62
A
MET
63
n
64
MET
63
A
ALA
64
n
65
ALA
64
A
VAL
65
n
66
VAL
65
A
ILE
66
n
67
ILE
66
A
TRP
67
n
68
TRP
67
A
GLU
68
n
69
GLU
68
A
GLU
69
n
70
GLU
69
A
ASN
70
n
71
ASN
70
A
THR
71
n
72
THR
71
A
LEU
72
n
73
LEU
72
A
TYR
73
n
74
TYR
73
A
ASP
74
n
75
ASP
74
A
TYR
75
n
76
TYR
75
A
LEU
76
n
77
LEU
76
A
LEU
77
n
78
LEU
77
A
ASN
78
n
79
ASN
78
A
PRO
79
n
80
PRO
79
A
LYS
80
n
81
M3L
80
A
LYS
81
n
82
LYS
81
A
TYR
82
n
83
TYR
82
A
ILE
83
n
84
ILE
83
A
PRO
84
n
85
PRO
84
A
GLY
85
n
86
GLY
85
A
THR
86
n
87
THR
86
A
LYS
87
n
88
LYS
87
A
MET
88
n
89
MET
88
A
VAL
89
n
90
VAL
89
A
PHE
90
n
91
PHE
90
A
PRO
91
n
92
PRO
91
A
GLY
92
n
93
GLY
92
A
LEU
93
n
94
LEU
93
A
LYS
94
n
95
M3L
94
A
LYS
95
n
96
LYS
95
A
PRO
96
n
97
PRO
96
A
GLN
97
n
98
GLN
97
A
GLU
98
n
99
GLU
98
A
ARG
99
n
100
ARG
99
A
ALA
100
n
101
ALA
100
A
ASP
101
n
102
ASP
101
A
LEU
102
n
103
LEU
102
A
ILE
103
n
104
ILE
103
A
SER
104
n
105
SER
104
A
TYR
105
n
106
TYR
105
A
LEU
106
n
107
LEU
106
A
LYS
107
n
108
LYS
107
A
GLU
108
n
109
GLU
108
A
ALA
109
n
110
ALA
109
A
THR
110
n
111
THR
110
A
SER
111
n
112
SER
111
A
author_defined_assembly
1
monomeric
A
HIS
26
A
NE2
HIS
27
1_555
A
HEC
112
B
FE
HEC
1_555
A
HEC
112
B
NA
HEC
1_555
91.3
A
HIS
26
A
NE2
HIS
27
1_555
A
HEC
112
B
FE
HEC
1_555
A
HEC
112
B
NB
HEC
1_555
86.1
A
HEC
112
B
NA
HEC
1_555
A
HEC
112
B
FE
HEC
1_555
A
HEC
112
B
NB
HEC
1_555
91.3
A
HIS
26
A
NE2
HIS
27
1_555
A
HEC
112
B
FE
HEC
1_555
A
HEC
112
B
NC
HEC
1_555
85.7
A
HEC
112
B
NA
HEC
1_555
A
HEC
112
B
FE
HEC
1_555
A
HEC
112
B
NC
HEC
1_555
176.7
A
HEC
112
B
NB
HEC
1_555
A
HEC
112
B
FE
HEC
1_555
A
HEC
112
B
NC
HEC
1_555
89.9
A
HIS
26
A
NE2
HIS
27
1_555
A
HEC
112
B
FE
HEC
1_555
A
HEC
112
B
ND
HEC
1_555
90.2
A
HEC
112
B
NA
HEC
1_555
A
HEC
112
B
FE
HEC
1_555
A
HEC
112
B
ND
HEC
1_555
90.5
A
HEC
112
B
NB
HEC
1_555
A
HEC
112
B
FE
HEC
1_555
A
HEC
112
B
ND
HEC
1_555
175.9
A
HEC
112
B
NC
HEC
1_555
A
HEC
112
B
FE
HEC
1_555
A
HEC
112
B
ND
HEC
1_555
88.1
A
HIS
26
A
NE2
HIS
27
1_555
A
HEC
112
B
FE
HEC
1_555
A
MET
88
A
SD
MET
89
1_555
178.3
A
HEC
112
B
NA
HEC
1_555
A
HEC
112
B
FE
HEC
1_555
A
MET
88
A
SD
MET
89
1_555
88.7
A
HEC
112
B
NB
HEC
1_555
A
HEC
112
B
FE
HEC
1_555
A
MET
88
A
SD
MET
89
1_555
95.6
A
HEC
112
B
NC
HEC
1_555
A
HEC
112
B
FE
HEC
1_555
A
MET
88
A
SD
MET
89
1_555
94.3
A
HEC
112
B
ND
HEC
1_555
A
HEC
112
B
FE
HEC
1_555
A
MET
88
A
SD
MET
89
1_555
88.1
A
M3L
80
N-TRIMETHYLLYSINE
A
M3L
81
LYS
A
M3L
94
N-TRIMETHYLLYSINE
A
M3L
95
LYS
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
ARG
46
0.149
SIDE CHAIN
1
15.74
2.20
113.40
129.14
A
A
A
CA
CB
CG
GLU
GLU
GLU
5
5
5
N
1
15.68
2.20
113.40
129.08
A
A
A
CA
CB
CG
LYS
LYS
LYS
12
12
12
N
1
-11.13
1.10
119.40
108.27
A
A
A
NH1
CZ
NH2
ARG
ARG
ARG
46
46
46
N
1
6.94
0.50
120.30
127.24
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
46
46
46
N
1
3.05
0.50
120.30
123.35
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
46
46
46
N
1
12.10
2.00
118.30
130.40
A
A
A
CG
CD
OE1
GLU
GLU
GLU
68
68
68
N
1
22.93
2.10
111.80
134.73
A
A
A
CG
CD
NE
ARG
ARG
ARG
99
99
99
N
1
33.37
1.40
123.60
156.97
A
A
A
CD
NE
CZ
ARG
ARG
ARG
99
99
99
N
1
4.90
0.50
120.30
125.20
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
99
99
99
N
1
-8.67
0.50
120.30
111.63
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
99
99
99
N
1
13.70
2.20
113.40
127.10
A
A
A
CA
CB
CG
GLU
GLU
GLU
108
108
108
N
1
16.77
2.70
114.20
130.97
A
A
A
CB
CG
CD
GLU
GLU
GLU
108
108
108
N
1
A
A
CD
NE
ARG
ARG
99
99
-0.158
0.017
1.460
1.302
N
1
A
A
CE
O
MET
HOH
63
118
1.23
1_555
6_555
1
A
A
O
O
HOH
HOH
128
133
2.04
1_555
6_665
1
A
LYS
35
-131.68
-143.07
1
A
ASN
78
-166.77
86.27
0.1900000
1.5
1
1.5
46
953
49
0
858
0.02
CYTOCHROME C
STRUCTURE OF RICE FERRICYTOCHROME C AT 2.0 ANGSTROMS RESOLUTION
1
N
N
2
N
N
3
N
N
A
ASN
10
A
ASN
11
HELX_P
A
CYS
22
A
CYS
23
1
H1
13
A
SER
57
A
SER
58
HELX_P
A
MET
63
A
MET
64
1
H2
7
A
GLU
68
A
GLU
69
HELX_P
A
ASN
78
A
ASN
79
1
H3
11
A
ASN
78
A
ASN
79
HELX_P
A
ILE
83
A
ILE
84
1
H4
6
A
LYS
95
A
LYS
96
HELX_P
A
SER
111
A
SER
112
1
H5
17
covale
1.335
both
A
ACE
0
A
C
ACE
1
1_555
A
ALA
1
A
N
ALA
2
1_555
covale
1.914
none
A
CYS
22
A
SG
CYS
23
1_555
A
HEC
112
B
CAB
HEC
1_555
covale
1.965
none
A
CYS
25
A
SG
CYS
26
1_555
A
HEC
112
B
CAC
HEC
1_555
covale
1.295
both
A
PRO
79
A
C
PRO
80
1_555
A
M3L
80
A
N
M3L
81
1_555
covale
1.311
both
A
M3L
80
A
C
M3L
81
1_555
A
LYS
81
A
N
LYS
82
1_555
covale
1.300
both
A
LEU
93
A
C
LEU
94
1_555
A
M3L
94
A
N
M3L
95
1_555
covale
1.311
both
A
M3L
94
A
C
M3L
95
1_555
A
LYS
95
A
N
LYS
96
1_555
metalc
2.037
A
HIS
26
A
NE2
HIS
27
1_555
A
HEC
112
B
FE
HEC
1_555
metalc
2.351
A
MET
88
A
SD
MET
89
1_555
A
HEC
112
B
FE
HEC
1_555
ELECTRON TRANSPORT(CYTOCHROME)
ELECTRON TRANSPORT(CYTOCHROME)
CYC_ORYSA
UNP
1
1
P00055
ASFSEAPPGNPKAGEKIFKTKCAQCHTVDKGAGHKQGPNLNGLFGRQSGTTPGYSYSTANKNMAVIWEENTLYDYLLNPK
KYIPGTKMVFPGLKKPQERADLISYLKEATS
1
111
1CCR
1
111
P00055
A
1
2
112
1
ASN
conflict
ASP
60
1CCR
A
P00055
UNP
60
61
BINDING SITE FOR RESIDUE HEC A 112
A
HEC
112
Software
23
A
LYS
21
A
LYS
22
23
1_555
A
CYS
22
A
CYS
23
23
1_555
A
CYS
25
A
CYS
26
23
1_555
A
HIS
26
A
HIS
27
23
1_555
A
GLN
36
A
GLN
37
23
1_555
A
GLY
37
A
GLY
38
23
1_555
A
PRO
38
A
PRO
39
23
1_555
A
SER
48
A
SER
49
23
1_555
A
GLY
49
A
GLY
50
23
1_555
A
TYR
54
A
TYR
55
23
1_555
A
TYR
56
A
TYR
57
23
1_555
A
SER
57
A
SER
58
23
1_555
A
ASP
60
A
ASP
61
23
1_555
A
TRP
67
A
TRP
68
23
1_555
A
TYR
75
A
TYR
76
23
1_555
A
THR
86
A
THR
87
23
1_555
A
LYS
87
A
LYS
88
23
1_555
A
MET
88
A
MET
89
23
1_555
A
VAL
89
A
VAL
90
23
1_555
A
PHE
90
A
PHE
91
23
1_555
A
LEU
102
A
LEU
103
23
1_555
A
HOH
123
C
HOH
23
1_555
A
HOH
135
C
HOH
23
1_555
169
P 61