1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Hasegawa, J.
Yoshida, T.
Yamazaki, T.
Sambongi, Y.
Yu, Y.
Igarashi, Y.
Kodama, T.
Yamazaki, K.
Hakusui, H.
Kyogoku, Y.
Kobayashi, Y.
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
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
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
US
Biochemistry
BICHAW
0033
0006-2960
37
9641
9649
10.1021/bi9803067
9657676
Solution structure of thermostable cytochrome c-552 from Hydrogenobacter thermophilus determined by 1H-NMR spectroscopy.
1998
10.2210/pdb1ayg/pdb
pdb_00001ayg
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
C-TYPE CYTOCHROME (REDUCED FORM)
8586.015
CYTOCHROME C-552
1
nat
polymer
618.503
HEME C
1
syn
non-polymer
no
no
NEQLAKQKGCMACHDLKAKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSIK
NEQLAKQKGCMACHDLKAKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSIK
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
Hydrogenobacter
sample
PERIPLASM
940
Hydrogenobacter thermophilus
TK-6
database_2
pdbx_database_status
pdbx_nmr_exptl_sample_conditions
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Experimental preparation
Other
1
0
1998-11-25
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_pdbx_nmr_exptl_sample_conditions.pressure_units
_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_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
BNL
1997-11-04
REL
HEC
HEME C
THE STRUCTURE WAS DETERMINED USING 1H-NMR SPECTROSCOPY ON CYTOCHROME C-552
LOWER ENERGY
100
20
NOESY
DQF-COSY
TOCSY
E.COSY
120mM ACETATE
4.8
1
atm
298
K
SIMULATED ANNEALING REFINEMENT FOR NMR STRUCTURE DETERMINATION.
simulated annealing
90% H2O/10% D2O, OR 99.98% D2O CONTAINING 120MM DEUTERATED ACETATE BUFFER
BRUNGER
refinement
X-PLOR
3.1
structure solution
X-PLOR
500
Bruker
ARX500
750
Bruker
AMX500 & DMX750
HEC
81
2
HEC
HEC
81
A
ASN
1
n
1
ASN
1
A
GLU
2
n
2
GLU
2
A
GLN
3
n
3
GLN
3
A
LEU
4
n
4
LEU
4
A
ALA
5
n
5
ALA
5
A
LYS
6
n
6
LYS
6
A
GLN
7
n
7
GLN
7
A
LYS
8
n
8
LYS
8
A
GLY
9
n
9
GLY
9
A
CYS
10
n
10
CYS
10
A
MET
11
n
11
MET
11
A
ALA
12
n
12
ALA
12
A
CYS
13
n
13
CYS
13
A
HIS
14
n
14
HIS
14
A
ASP
15
n
15
ASP
15
A
LEU
16
n
16
LEU
16
A
LYS
17
n
17
LYS
17
A
ALA
18
n
18
ALA
18
A
LYS
19
n
19
LYS
19
A
LYS
20
n
20
LYS
20
A
VAL
21
n
21
VAL
21
A
GLY
22
n
22
GLY
22
A
PRO
23
n
23
PRO
23
A
ALA
24
n
24
ALA
24
A
TYR
25
n
25
TYR
25
A
ALA
26
n
26
ALA
26
A
ASP
27
n
27
ASP
27
A
VAL
28
n
28
VAL
28
A
ALA
29
n
29
ALA
29
A
LYS
30
n
30
LYS
30
A
LYS
31
n
31
LYS
31
A
TYR
32
n
32
TYR
32
A
ALA
33
n
33
ALA
33
A
GLY
34
n
34
GLY
34
A
ARG
35
n
35
ARG
35
A
LYS
36
n
36
LYS
36
A
ASP
37
n
37
ASP
37
A
ALA
38
n
38
ALA
38
A
VAL
39
n
39
VAL
39
A
ASP
40
n
40
ASP
40
A
TYR
41
n
41
TYR
41
A
LEU
42
n
42
LEU
42
A
ALA
43
n
43
ALA
43
A
GLY
44
n
44
GLY
44
A
LYS
45
n
45
LYS
45
A
ILE
46
n
46
ILE
46
A
LYS
47
n
47
LYS
47
A
LYS
48
n
48
LYS
48
A
GLY
49
n
49
GLY
49
A
GLY
50
n
50
GLY
50
A
SER
51
n
51
SER
51
A
GLY
52
n
52
GLY
52
A
VAL
53
n
53
VAL
53
A
TRP
54
n
54
TRP
54
A
GLY
55
n
55
GLY
55
A
SER
56
n
56
SER
56
A
VAL
57
n
57
VAL
57
A
PRO
58
n
58
PRO
58
A
MET
59
n
59
MET
59
A
PRO
60
n
60
PRO
60
A
PRO
61
n
61
PRO
61
A
GLN
62
n
62
GLN
62
A
ASN
63
n
63
ASN
63
A
VAL
64
n
64
VAL
64
A
THR
65
n
65
THR
65
A
ASP
66
n
66
ASP
66
A
ALA
67
n
67
ALA
67
A
GLU
68
n
68
GLU
68
A
ALA
69
n
69
ALA
69
A
LYS
70
n
70
LYS
70
A
GLN
71
n
71
GLN
71
A
LEU
72
n
72
LEU
72
A
ALA
73
n
73
ALA
73
A
GLN
74
n
74
GLN
74
A
TRP
75
n
75
TRP
75
A
ILE
76
n
76
ILE
76
A
LEU
77
n
77
LEU
77
A
SER
78
n
78
SER
78
A
ILE
79
n
79
ILE
79
A
LYS
80
n
80
LYS
80
A
author_defined_assembly
1
monomeric
A
HIS
14
A
NE2
HIS
14
1_555
A
HEC
81
B
FE
HEC
1_555
A
HEC
81
B
NA
HEC
1_555
72.8
A
HIS
14
A
NE2
HIS
14
1_555
A
HEC
81
B
FE
HEC
1_555
A
HEC
81
B
NB
HEC
1_555
105.3
A
HEC
81
B
NA
HEC
1_555
A
HEC
81
B
FE
HEC
1_555
A
HEC
81
B
NB
HEC
1_555
90.0
A
HIS
14
A
NE2
HIS
14
1_555
A
HEC
81
B
FE
HEC
1_555
A
HEC
81
B
NC
HEC
1_555
105.8
A
HEC
81
B
NA
HEC
1_555
A
HEC
81
B
FE
HEC
1_555
A
HEC
81
B
NC
HEC
1_555
178.5
A
HEC
81
B
NB
HEC
1_555
A
HEC
81
B
FE
HEC
1_555
A
HEC
81
B
NC
HEC
1_555
90.0
A
HIS
14
A
NE2
HIS
14
1_555
A
HEC
81
B
FE
HEC
1_555
A
HEC
81
B
ND
HEC
1_555
74.4
A
HEC
81
B
NA
HEC
1_555
A
HEC
81
B
FE
HEC
1_555
A
HEC
81
B
ND
HEC
1_555
90.2
A
HEC
81
B
NB
HEC
1_555
A
HEC
81
B
FE
HEC
1_555
A
HEC
81
B
ND
HEC
1_555
179.7
A
HEC
81
B
NC
HEC
1_555
A
HEC
81
B
FE
HEC
1_555
A
HEC
81
B
ND
HEC
1_555
89.9
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
GLU
2
-157.07
-41.75
1
A
ASP
15
163.63
148.74
1
A
LEU
16
-50.39
-75.68
1
A
ALA
18
-118.39
67.58
1
A
LYS
20
-128.96
-95.72
1
A
VAL
21
-94.27
-72.81
1
A
ALA
33
163.59
109.91
1
A
LEU
42
-56.78
-70.87
1
A
LYS
48
-129.79
-59.97
1
A
SER
51
179.50
167.65
1
A
ASN
63
-104.09
78.07
2
A
GLU
2
-178.69
-40.08
2
A
ASP
15
161.07
136.12
2
A
LYS
20
-140.39
-56.46
2
A
TYR
32
-109.94
-132.57
2
A
ALA
33
78.50
107.67
2
A
ASP
37
-94.27
39.08
2
A
LEU
42
-65.14
-70.09
2
A
SER
51
169.49
56.50
2
A
VAL
57
-50.01
106.98
3
A
GLN
3
173.06
-42.62
3
A
HIS
14
-108.39
-169.38
3
A
ASP
15
162.69
135.95
3
A
TYR
32
-96.61
-115.57
3
A
ALA
33
76.66
106.97
3
A
ASN
63
-104.57
57.22
4
A
GLN
3
82.73
-43.29
4
A
HIS
14
-69.87
-171.39
4
A
ASP
15
169.98
132.28
4
A
LEU
16
-42.65
-70.05
4
A
ALA
18
-153.70
59.46
4
A
LYS
19
-48.92
101.79
4
A
ALA
33
170.47
-32.81
4
A
VAL
57
-46.17
104.60
4
A
ASN
63
-96.32
55.15
5
A
GLN
3
168.65
-75.29
5
A
ASP
15
-160.44
23.27
5
A
LEU
16
81.36
-59.32
5
A
LYS
19
-51.17
97.09
5
A
LYS
20
-113.16
-89.37
5
A
ILE
46
-102.20
-60.03
5
A
SER
51
179.81
150.76
5
A
VAL
57
-43.66
107.61
5
A
GLN
62
-100.46
-162.79
5
A
ASN
63
-117.69
65.84
5
A
ILE
79
-47.85
100.05
6
A
GLU
2
-176.41
-44.20
6
A
LYS
6
-88.92
-73.75
6
A
ASP
15
-178.94
139.66
6
A
ALA
18
53.86
109.01
6
A
LYS
19
172.91
59.71
6
A
LYS
20
-171.65
-176.19
6
A
ALA
24
-49.73
153.23
6
A
ALA
33
168.61
107.93
6
A
ASP
37
-174.86
50.31
6
A
LYS
48
-159.35
64.57
6
A
VAL
57
-48.35
109.99
7
A
GLU
2
-113.10
71.60
7
A
GLN
3
-175.11
-47.69
7
A
CYS
13
-131.64
-39.37
7
A
HIS
14
-74.87
-168.63
7
A
ASP
15
166.86
136.15
7
A
LYS
19
-42.64
100.66
7
A
VAL
21
-126.96
-68.67
7
A
TYR
32
-112.39
-127.55
7
A
ALA
33
80.35
108.00
7
A
LYS
48
-142.25
11.77
7
A
SER
51
174.74
94.92
7
A
ASN
63
-97.33
58.87
7
A
ILE
79
-62.06
99.72
8
A
GLN
3
84.04
-25.75
8
A
GLN
7
-56.75
-74.77
8
A
ASP
15
162.78
123.16
8
A
ALA
18
-164.35
49.96
8
A
LYS
19
-49.49
164.94
8
A
LYS
20
-150.09
-65.10
8
A
TYR
32
-107.71
-139.96
8
A
ALA
33
83.37
112.80
8
A
LYS
48
-108.03
-77.46
8
A
SER
51
179.02
156.20
8
A
TRP
54
-134.08
-30.71
8
A
ASN
63
-110.53
72.77
9
A
GLN
3
-142.82
-43.31
9
A
ASP
15
166.99
120.68
9
A
ALA
18
-152.78
72.43
9
A
LYS
20
-116.59
-77.13
9
A
ALA
33
160.78
109.78
9
A
LYS
48
-144.23
31.42
9
A
SER
51
174.89
90.98
9
A
VAL
57
-41.56
101.70
9
A
ILE
79
-69.79
92.11
10
A
GLU
2
-171.32
-40.93
10
A
CYS
13
-133.45
-40.04
10
A
ASP
15
163.47
119.37
10
A
LYS
20
-142.16
-69.43
10
A
TYR
32
-104.38
-149.87
10
A
ALA
33
84.10
-33.73
10
A
LYS
36
-96.88
33.68
10
A
ASP
37
169.66
45.18
10
A
LYS
48
-123.33
-71.70
10
A
SER
51
177.22
144.18
11
A
ASP
15
164.39
129.02
11
A
LYS
20
-160.26
-97.05
11
A
TYR
32
-125.64
-145.57
11
A
ALA
33
81.92
109.82
11
A
ARG
35
-82.97
36.92
11
A
LYS
36
69.73
-4.70
11
A
ASP
37
167.05
52.87
11
A
LEU
42
-47.13
-75.90
11
A
SER
51
168.27
81.80
11
A
ASN
63
-88.67
47.16
12
A
GLU
2
-179.57
-34.78
12
A
ASP
15
173.19
136.25
12
A
ALA
18
-152.73
81.32
12
A
LYS
19
-55.16
90.50
12
A
LYS
20
-89.97
-156.52
12
A
TYR
32
-98.27
-101.89
12
A
ALA
33
72.37
104.97
12
A
SER
51
-173.65
143.32
12
A
ASN
63
-102.15
60.98
13
A
GLN
3
169.95
-44.77
13
A
ASP
15
-176.80
145.77
13
A
ALA
18
55.39
-179.29
13
A
LYS
19
70.53
101.72
13
A
LYS
20
167.22
-166.65
13
A
TYR
32
-104.37
-111.63
13
A
ALA
33
75.07
105.63
13
A
LYS
48
-111.80
-76.88
13
A
ASN
63
-115.86
76.00
14
A
GLU
2
-118.77
75.67
14
A
GLN
3
-157.47
-55.22
14
A
ASP
15
162.74
135.01
14
A
LYS
20
-131.56
-95.80
14
A
ALA
24
-49.93
155.84
14
A
SER
51
177.87
84.26
14
A
TRP
54
-144.83
35.63
14
A
VAL
57
-43.30
103.61
15
A
GLU
2
49.26
85.24
15
A
GLN
3
-170.66
-62.31
15
A
HIS
14
-62.09
-174.86
15
A
ASP
15
170.70
127.11
15
A
LEU
16
-42.36
-71.73
15
A
LYS
20
-91.71
-74.46
15
A
TYR
32
-88.94
-103.50
15
A
ALA
33
75.40
106.98
15
A
LYS
48
-126.71
-78.84
16
A
GLN
3
-170.05
-37.32
16
A
GLN
7
-53.92
-79.35
16
A
ASP
15
166.69
136.23
16
A
LYS
19
-61.47
98.26
16
A
LYS
20
-109.07
-97.76
16
A
TYR
32
-123.64
-144.42
16
A
ALA
33
78.96
107.46
16
A
ARG
35
-61.06
-163.66
16
A
ASP
37
178.77
70.86
16
A
SER
51
176.04
159.57
16
A
VAL
57
-46.38
106.62
17
A
GLN
3
179.74
-48.94
17
A
ASP
15
164.29
124.02
17
A
ALA
18
-158.10
58.56
17
A
LYS
20
-122.81
-105.45
17
A
TYR
32
-106.55
-143.63
17
A
ALA
33
83.55
-37.70
17
A
ASP
37
-178.85
44.92
17
A
LYS
48
-104.25
-72.68
18
A
GLU
2
-165.30
62.94
18
A
GLN
3
-172.25
-49.42
18
A
LYS
6
-54.78
-71.74
18
A
ASP
15
164.68
126.61
18
A
LYS
19
-53.02
108.97
18
A
LYS
20
-114.06
-147.20
18
A
TYR
32
-106.88
-142.65
18
A
ALA
33
80.98
107.38
18
A
LYS
48
-125.01
-66.70
18
A
SER
56
-113.16
51.60
18
A
ASN
63
-109.34
52.07
19
A
GLU
2
179.93
42.30
19
A
ASP
15
175.58
137.21
19
A
ALA
18
49.31
98.34
19
A
LYS
19
171.04
88.34
19
A
LYS
20
175.26
-153.31
19
A
TYR
32
-101.44
-123.44
19
A
ALA
33
81.24
109.95
19
A
LYS
48
-149.18
-71.67
19
A
SER
51
179.25
143.57
19
A
TRP
54
-152.66
33.15
19
A
ASN
63
-98.86
50.07
20
A
GLU
2
46.34
86.40
20
A
GLN
3
179.17
-54.21
20
A
ASP
15
164.06
147.94
20
A
ALA
18
-140.44
55.10
20
A
LYS
20
-122.52
-91.39
20
A
ALA
33
175.32
107.80
20
A
LYS
48
-146.66
-46.19
20
A
SER
56
-95.61
41.72
20
A
GLN
62
-118.86
-166.62
20
A
ASN
63
-113.19
77.62
model building
X-PLOR
3.1
refinement
X-PLOR
3.1
phasing
X-PLOR
3.1
SOLUTION STRUCTURE OF CYTOCHROME C-552, NMR, 20 STRUCTURES
1
Y
N
2
N
N
A
GLN
3
A
GLN
3
HELX_P
A
GLN
7
A
GLN
7
1
1
5
A
TYR
25
A
TYR
25
HELX_P
A
TYR
32
A
TYR
32
1
2
8
A
ALA
38
A
ALA
38
HELX_P
A
LYS
47
A
LYS
47
1
3
10
A
ALA
67
A
ALA
67
HELX_P
A
SER
78
A
SER
78
1
4
12
covale
1.812
none
A
CYS
10
A
SG
CYS
10
1_555
A
HEC
81
B
CAB
HEC
1_555
covale
1.813
none
A
CYS
13
A
SG
CYS
13
1_555
A
HEC
81
B
CAC
HEC
1_555
metalc
2.984
A
HIS
14
A
NE2
HIS
14
1_555
A
HEC
81
B
FE
HEC
1_555
ELECTRON TRANSPORT
CYTOCHROME C, ELECTRON TRANSPORT, PORPHYRIN, FERROUS IRON
CY552_HYDTH
UNP
1
1
P15452
MKKFLLVAVVGLAGITFANEQLAKQKGCMACHDLKAKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQ
NVTDAEAKQLAQWILSIK
19
98
1AYG
1
80
P15452
A
1
1
80
BINDING SITE FOR RESIDUE HEC A 81
A
HEC
81
Software
14
A
GLY
9
A
GLY
9
14
1_555
A
CYS
10
A
CYS
10
14
1_555
A
CYS
13
A
CYS
13
14
1_555
A
HIS
14
A
HIS
14
14
1_555
A
PRO
23
A
PRO
23
14
1_555
A
TYR
32
A
TYR
32
14
1_555
A
ILE
46
A
ILE
46
14
1_555
A
GLY
52
A
GLY
52
14
1_555
A
TRP
54
A
TRP
54
14
1_555
A
GLY
55
A
GLY
55
14
1_555
A
VAL
57
A
VAL
57
14
1_555
A
MET
59
A
MET
59
14
1_555
A
GLN
62
A
GLN
62
14
1_555
A
LEU
72
A
LEU
72
14
1_555
1
P 1