1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Arnesano, F.
Banci, L.
Bertini, I.
Koulougliotis, 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
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 H32 Fe N4 O4
616.487
PROTOPORPHYRIN IX CONTAINING FE
HEME
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
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
US
Biochemistry
BICHAW
0033
0006-2960
37
17082
17092
10.1021/bi981546p
9836603
Solution structure of oxidized rat microsomal cytochrome b5 in the presence of 2 M guanidinium chloride: monitoring the early steps in protein unfolding.
1998
10.2210/pdb1blv/pdb
pdb_00001blv
CHIRALITY ERROR AT CA OF ASP 1 A
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
10813.908
PROTEIN (CYTOCHROME B5)
SOLUBLE DOMAIN
1
man
polymer
616.487
PROTOPORPHYRIN IX CONTAINING FE
1
syn
non-polymer
no
no
DKDVKYYTLEEIQKHKDSKSTWVILHHKVYDLTKFLEEHPGGEEVLREQAGGDATENFEDVGHSTDARELSKTYIIGELH
PDDRSKIAKPSETL
DKDVKYYTLEEIQKHKDSKSTWVILHHKVYDLTKFLEEHPGGEEVLREQAGGDATENFEDVGHSTDARELSKTYIIGELH
PDDRSKIAKPSETL
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
Norway rat
Rattus
Escherichia
sample
10116
LIVER
MICROSOME
Rattus norvegicus
CYTOPLASM
562
Escherichia coli
NM522
PLASMID
PUC 13
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
1998-07-29
1
1
2007-10-16
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
BNL
Y
RCSB
1998-07-21
REL
HEM
PROTOPORPHYRIN IX CONTAINING FE
MEAN STRUCTURE
MINIMIZED AVERAGE STRUCTURE
40
1
NOESY
TOCSY
PHOSPHATE BUFFER 100 mM PLUS 2 M GDMCL IN THE SAME BUFFER
7
1
atm
298
K
PSEUDOREM (BANCI,BERTINI,GORI SAVELLINI,ROMAGNOLI,TURANO, CREMONINI,LUCHINAT, GRAY) ALSO WAS USED.
TORSION ANGLE MOLECULAR DYNAMICS SIMULATED ANNEALING, RESTRAINED ENERGY MINIMIZATION; PSEUDOCONTACT SHIFTS WERE USED IN THE CALCULATION AND IN THE MINIMIZATION AS FURTHER NON-CLASSICAL CONSTRAINTS
PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMAN
refinement
Amber
structure solution
DYANA
structure solution
PSEUDYANA
structure solution
Amber
500
Bruker
DRX 500
HEM
96
2
HEM
HEM
96
A
ASP
1
n
1
ASP
1
A
LYS
2
n
2
LYS
2
A
ASP
3
n
3
ASP
3
A
VAL
4
n
4
VAL
4
A
LYS
5
n
5
LYS
5
A
TYR
6
n
6
TYR
6
A
TYR
7
n
7
TYR
7
A
THR
8
n
8
THR
8
A
LEU
9
n
9
LEU
9
A
GLU
10
n
10
GLU
10
A
GLU
11
n
11
GLU
11
A
ILE
12
n
12
ILE
12
A
GLN
13
n
13
GLN
13
A
LYS
14
n
14
LYS
14
A
HIS
15
n
15
HIS
15
A
LYS
16
n
16
LYS
16
A
ASP
17
n
17
ASP
17
A
SER
18
n
18
SER
18
A
LYS
19
n
19
LYS
19
A
SER
20
n
20
SER
20
A
THR
21
n
21
THR
21
A
TRP
22
n
22
TRP
22
A
VAL
23
n
23
VAL
23
A
ILE
24
n
24
ILE
24
A
LEU
25
n
25
LEU
25
A
HIS
26
n
26
HIS
26
A
HIS
27
n
27
HIS
27
A
LYS
28
n
28
LYS
28
A
VAL
29
n
29
VAL
29
A
TYR
30
n
30
TYR
30
A
ASP
31
n
31
ASP
31
A
LEU
32
n
32
LEU
32
A
THR
33
n
33
THR
33
A
LYS
34
n
34
LYS
34
A
PHE
35
n
35
PHE
35
A
LEU
36
n
36
LEU
36
A
GLU
37
n
37
GLU
37
A
GLU
38
n
38
GLU
38
A
HIS
39
n
39
HIS
39
A
PRO
40
n
40
PRO
40
A
GLY
41
n
41
GLY
41
A
GLY
42
n
42
GLY
42
A
GLU
43
n
43
GLU
43
A
GLU
44
n
44
GLU
44
A
VAL
45
n
45
VAL
45
A
LEU
46
n
46
LEU
46
A
ARG
47
n
47
ARG
47
A
GLU
48
n
48
GLU
48
A
GLN
49
n
49
GLN
49
A
ALA
50
n
50
ALA
50
A
GLY
51
n
51
GLY
51
A
GLY
52
n
52
GLY
52
A
ASP
53
n
53
ASP
53
A
ALA
54
n
54
ALA
54
A
THR
55
n
55
THR
55
A
GLU
56
n
56
GLU
56
A
ASN
57
n
57
ASN
57
A
PHE
58
n
58
PHE
58
A
GLU
59
n
59
GLU
59
A
ASP
60
n
60
ASP
60
A
VAL
61
n
61
VAL
61
A
GLY
62
n
62
GLY
62
A
HIS
63
n
63
HIS
63
A
SER
64
n
64
SER
64
A
THR
65
n
65
THR
65
A
ASP
66
n
66
ASP
66
A
ALA
67
n
67
ALA
67
A
ARG
68
n
68
ARG
68
A
GLU
69
n
69
GLU
69
A
LEU
70
n
70
LEU
70
A
SER
71
n
71
SER
71
A
LYS
72
n
72
LYS
72
A
THR
73
n
73
THR
73
A
TYR
74
n
74
TYR
74
A
ILE
75
n
75
ILE
75
A
ILE
76
n
76
ILE
76
A
GLY
77
n
77
GLY
77
A
GLU
78
n
78
GLU
78
A
LEU
79
n
79
LEU
79
A
HIS
80
n
80
HIS
80
A
PRO
81
n
81
PRO
81
A
ASP
82
n
82
ASP
82
A
ASP
83
n
83
ASP
83
A
ARG
84
n
84
ARG
84
A
SER
85
n
85
SER
85
A
LYS
86
n
86
LYS
86
A
ILE
87
n
87
ILE
87
A
ALA
88
n
88
ALA
88
A
LYS
89
n
89
LYS
89
A
PRO
90
n
90
PRO
90
A
SER
91
n
91
SER
91
A
GLU
92
n
92
GLU
92
A
THR
93
n
93
THR
93
A
LEU
94
n
94
LEU
94
A
author_defined_assembly
1
monomeric
A
HIS
39
A
NE2
HIS
39
1_555
A
HEM
96
B
FE
HEM
1_555
A
HEM
96
B
NA
HEM
1_555
92.4
A
HIS
39
A
NE2
HIS
39
1_555
A
HEM
96
B
FE
HEM
1_555
A
HEM
96
B
NB
HEM
1_555
92.0
A
HEM
96
B
NA
HEM
1_555
A
HEM
96
B
FE
HEM
1_555
A
HEM
96
B
NB
HEM
1_555
89.5
A
HIS
39
A
NE2
HIS
39
1_555
A
HEM
96
B
FE
HEM
1_555
A
HEM
96
B
NC
HEM
1_555
91.3
A
HEM
96
B
NA
HEM
1_555
A
HEM
96
B
FE
HEM
1_555
A
HEM
96
B
NC
HEM
1_555
176.2
A
HEM
96
B
NB
HEM
1_555
A
HEM
96
B
FE
HEM
1_555
A
HEM
96
B
NC
HEM
1_555
89.6
A
HIS
39
A
NE2
HIS
39
1_555
A
HEM
96
B
FE
HEM
1_555
A
HEM
96
B
ND
HEM
1_555
88.3
A
HEM
96
B
NA
HEM
1_555
A
HEM
96
B
FE
HEM
1_555
A
HEM
96
B
ND
HEM
1_555
91.0
A
HEM
96
B
NB
HEM
1_555
A
HEM
96
B
FE
HEM
1_555
A
HEM
96
B
ND
HEM
1_555
179.4
A
HEM
96
B
NC
HEM
1_555
A
HEM
96
B
FE
HEM
1_555
A
HEM
96
B
ND
HEM
1_555
89.9
A
HIS
39
A
NE2
HIS
39
1_555
A
HEM
96
B
FE
HEM
1_555
A
HIS
63
A
NE2
HIS
63
1_555
174.5
A
HEM
96
B
NA
HEM
1_555
A
HEM
96
B
FE
HEM
1_555
A
HIS
63
A
NE2
HIS
63
1_555
91.8
A
HEM
96
B
NB
HEM
1_555
A
HEM
96
B
FE
HEM
1_555
A
HIS
63
A
NE2
HIS
63
1_555
91.6
A
HEM
96
B
NC
HEM
1_555
A
HEM
96
B
FE
HEM
1_555
A
HIS
63
A
NE2
HIS
63
1_555
84.5
A
HEM
96
B
ND
HEM
1_555
A
HEM
96
B
FE
HEM
1_555
A
HIS
63
A
NE2
HIS
63
1_555
88.0
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
CA
ASP
1
WRONG HAND
1
A
A
ASP
SER
17
18
142.42
1
A
A
SER
GLU
91
92
119.44
1
A
TYR
7
0.116
SIDE CHAIN
1
A
PHE
35
0.084
SIDE CHAIN
1
A
TYR
74
0.240
SIDE CHAIN
1
19.90
2.80
113.90
133.80
A
A
A
CB
CG1
CD1
ILE
ILE
ILE
87
87
87
N
1
A
TYR
6
-57.85
107.28
1
A
LYS
16
-165.60
-54.72
1
A
SER
20
-153.89
83.51
1
A
ILE
24
-109.91
76.11
1
A
HIS
26
33.78
53.59
1
A
GLU
38
-159.40
-49.09
1
A
ALA
50
51.99
-128.09
1
A
ASP
53
-163.52
65.10
1
A
THR
55
-98.33
-65.74
1
A
SER
64
-113.93
-166.79
1
A
THR
65
57.07
-141.24
1
A
GLU
78
60.41
170.62
1
A
ASP
82
-60.29
-76.50
1
A
PRO
90
-67.56
-78.86
1
A
SER
91
174.15
149.46
1
A
GLU
92
42.40
132.76
1
A
THR
93
174.26
-46.89
SOLUTION STRUCTURE OF OXIDIZED RAT MICROSOMAL CYTOCHROME B5 IN THE PRESENCE OF 2 M GUANIDINIUM CHLORIDE: MONITORING THE EARLY STEPS IN PROTEIN UNFOLDING
1
N
N
2
N
N
A
THR
8
A
THR
8
HELX_P
A
GLN
13
A
GLN
13
1
1
6
A
LYS
34
A
LYS
34
HELX_P
A
GLU
38
A
GLU
38
5
2
5
A
GLU
43
A
GLU
43
HELX_P
A
ALA
50
A
ALA
50
1
3
8
A
THR
55
A
THR
55
HELX_P
A
GLY
62
A
GLY
62
1
4
8
A
SER
64
A
SER
64
HELX_P
A
LYS
72
A
LYS
72
1
5
9
A
PRO
81
A
PRO
81
HELX_P
A
LYS
86
A
LYS
86
1
6
6
metalc
1.987
A
HIS
39
A
NE2
HIS
39
1_555
A
HEM
96
B
FE
HEM
1_555
metalc
1.969
A
HIS
63
A
NE2
HIS
63
1_555
A
HEM
96
B
FE
HEM
1_555
ELECTRON TRANSPORT
PROTEIN UNFOLDING, NMR SOLUTION STRUCTURE, CYTOCHROME B5, ELECTRON TRANSPORT
A
GLU
92
A
GLU
92
1
A
THR
93
A
THR
93
13.96
CYB5_RAT
UNP
1
P00173
5
98
1BLV
1
94
P00173
A
1
1
94
1
1
A
THR
21
A
THR
21
A
LEU
25
A
LEU
25
A
LYS
28
A
LYS
28
A
LEU
32
A
LEU
32
HEME RING (B-TYPE) CONTAINS LOW-SPIN FERRIC ION
Author
2
BINDING SITE FOR RESIDUE HEM A 96
A
HEM
96
Software
10
A
HIS
39
A
HIS
39
2
1_555
A
HIS
63
A
HIS
63
2
1_555
A
LEU
32
A
LEU
32
10
1_555
A
HIS
39
A
HIS
39
10
1_555
A
PRO
40
A
PRO
40
10
1_555
A
VAL
45
A
VAL
45
10
1_555
A
LEU
46
A
LEU
46
10
1_555
A
PHE
58
A
PHE
58
10
1_555
A
HIS
63
A
HIS
63
10
1_555
A
ALA
67
A
ALA
67
10
1_555
A
SER
71
A
SER
71
10
1_555
A
TYR
74
A
TYR
74
10
1_555
1
P 1