0.033333
0.000000
0.000000
0.000000
0.033333
0.000000
0.000000
0.000000
0.004566
0.00000
0.00000
0.00000
Rivera, M.
White, S.P.
Zhang, X.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
30.000
30.000
219.000
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
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
US
Biochemistry
BICHAW
0033
0006-2960
35
16378
16390
10.1021/bi961895o
8973214
13C NMR spectroscopic and X-ray crystallographic study of the role played by mitochondrial cytochrome b5 heme propionates in the electrostatic binding to cytochrome c.
1996
10.2210/pdb1b5m/pdb
pdb_00001b5m
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
298
1
AREA DETECTOR
1996-04-18
SIEMENS
DIAMOND C(111)
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
FROM RAT OUTER MITOCHONDRIAL MEMBRANE
9605.570
CYTOCHROME B5
WATER SOLUBLE DOMAIN
1
man
polymer
616.487
PROTOPORPHYRIN IX CONTAINING FE
1
syn
non-polymer
no
no
AVTYYRLEEVAKRNTAEETWMVIHGRVYDITRFLSEHPGGEEVLLEQAGADATESFEDVGHSPDAREMLKQYYIGDVHPN
DLKP
AVTYYRLEEVAKRNTAEETWMVIHGRVYDITRFLSEHPGGEEVLLEQAGADATESFEDVGHSPDAREMLKQYYIGDVHPN
DLKP
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
Norway rat
Rattus
Escherichia
Escherichia coli
sample
HEPATOCYTE
BL21
OUTER MITOCHONDRIAL MEMBRANE
10116
LIVER
MITOCHONDRION
Rattus norvegicus
PERIPLASMIC SPACE
469008
Escherichia coli BL21(DE3)
BL21 (DE3)
PLASMID
PET 11A
1
2.56
52.02
vapor diffusion with slow evaporation
6.5
CRYSTALS WERE OBTAINED BY VAPOR DIFFUSION TOGETHER WITH SLOW EVAPORATION USING 20% PEG 8000 IN 0.1M SODIUM CACODYLATE (PH = 6.5 WITH 0.2 M MAGNESIUM ACETATE., vapor diffusion with slow evaporation
database_2
pdbx_database_status
pdbx_initial_refinement_model
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
Refinement description
1
0
1997-03-12
1
1
2008-03-24
1
2
2011-07-13
1
3
2023-08-02
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_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
1996-11-07
REL
HEM
PROTOPORPHYRIN IX CONTAINING FE
3B5C
PDB ENTRY 3B5C
PDB
experimental model
HEM
201
2
HEM
HEM
201
A
ALA
3
n
1
ALA
3
A
VAL
4
n
2
VAL
4
A
THR
5
n
3
THR
5
A
TYR
6
n
4
TYR
6
A
TYR
7
n
5
TYR
7
A
ARG
8
n
6
ARG
8
A
LEU
9
n
7
LEU
9
A
GLU
10
n
8
GLU
10
A
GLU
11
n
9
GLU
11
A
VAL
12
n
10
VAL
12
A
ALA
13
n
11
ALA
13
A
LYS
14
n
12
LYS
14
A
ARG
15
n
13
ARG
15
A
ASN
16
n
14
ASN
16
A
THR
17
n
15
THR
17
A
ALA
18
n
16
ALA
18
A
GLU
19
n
17
GLU
19
A
GLU
20
n
18
GLU
20
A
THR
21
n
19
THR
21
A
TRP
22
n
20
TRP
22
A
MET
23
n
21
MET
23
A
VAL
24
n
22
VAL
24
A
ILE
25
n
23
ILE
25
A
HIS
26
n
24
HIS
26
A
GLY
27
n
25
GLY
27
A
ARG
28
n
26
ARG
28
A
VAL
29
n
27
VAL
29
A
TYR
30
n
28
TYR
30
A
ASP
31
n
29
ASP
31
A
ILE
32
n
30
ILE
32
A
THR
33
n
31
THR
33
A
ARG
34
n
32
ARG
34
A
PHE
35
n
33
PHE
35
A
LEU
36
n
34
LEU
36
A
SER
37
n
35
SER
37
A
GLU
38
n
36
GLU
38
A
HIS
39
n
37
HIS
39
A
PRO
40
n
38
PRO
40
A
GLY
41
n
39
GLY
41
A
GLY
42
n
40
GLY
42
A
GLU
43
n
41
GLU
43
A
GLU
44
n
42
GLU
44
A
VAL
45
n
43
VAL
45
A
LEU
46
n
44
LEU
46
A
LEU
47
n
45
LEU
47
A
GLU
48
n
46
GLU
48
A
GLN
49
n
47
GLN
49
A
ALA
50
n
48
ALA
50
A
GLY
51
n
49
GLY
51
A
ALA
52
n
50
ALA
52
A
ASP
53
n
51
ASP
53
A
ALA
54
n
52
ALA
54
A
THR
55
n
53
THR
55
A
GLU
56
n
54
GLU
56
A
SER
57
n
55
SER
57
A
PHE
58
n
56
PHE
58
A
GLU
59
n
57
GLU
59
A
ASP
60
n
58
ASP
60
A
VAL
61
n
59
VAL
61
A
GLY
62
n
60
GLY
62
A
HIS
63
n
61
HIS
63
A
SER
64
n
62
SER
64
A
PRO
65
n
63
PRO
65
A
ASP
66
n
64
ASP
66
A
ALA
67
n
65
ALA
67
A
ARG
68
n
66
ARG
68
A
GLU
69
n
67
GLU
69
A
MET
70
n
68
MET
70
A
LEU
71
n
69
LEU
71
A
LYS
72
n
70
LYS
72
A
GLN
73
n
71
GLN
73
A
TYR
74
n
72
TYR
74
A
TYR
75
n
73
TYR
75
A
ILE
76
n
74
ILE
76
A
GLY
77
n
75
GLY
77
A
ASP
78
n
76
ASP
78
A
VAL
79
n
77
VAL
79
A
HIS
80
n
78
HIS
80
A
PRO
81
n
79
PRO
81
A
ASN
82
n
80
ASN
82
A
ASP
83
n
81
ASP
83
A
LEU
84
n
82
LEU
84
A
LYS
85
n
83
LYS
85
A
PRO
86
n
84
PRO
86
A
0.2200000
author_defined_assembly
1
monomeric
A
HIS
39
A
NE2
HIS
37
1_555
A
HEM
201
B
FE
HEM
1_555
A
HEM
201
B
NA
HEM
1_555
85.7
A
HIS
39
A
NE2
HIS
37
1_555
A
HEM
201
B
FE
HEM
1_555
A
HEM
201
B
NB
HEM
1_555
98.9
A
HEM
201
B
NA
HEM
1_555
A
HEM
201
B
FE
HEM
1_555
A
HEM
201
B
NB
HEM
1_555
88.6
A
HIS
39
A
NE2
HIS
37
1_555
A
HEM
201
B
FE
HEM
1_555
A
HEM
201
B
NC
HEM
1_555
99.1
A
HEM
201
B
NA
HEM
1_555
A
HEM
201
B
FE
HEM
1_555
A
HEM
201
B
NC
HEM
1_555
175.2
A
HEM
201
B
NB
HEM
1_555
A
HEM
201
B
FE
HEM
1_555
A
HEM
201
B
NC
HEM
1_555
91.2
A
HIS
39
A
NE2
HIS
37
1_555
A
HEM
201
B
FE
HEM
1_555
A
HEM
201
B
ND
HEM
1_555
90.9
A
HEM
201
B
NA
HEM
1_555
A
HEM
201
B
FE
HEM
1_555
A
HEM
201
B
ND
HEM
1_555
89.6
A
HEM
201
B
NB
HEM
1_555
A
HEM
201
B
FE
HEM
1_555
A
HEM
201
B
ND
HEM
1_555
169.9
A
HEM
201
B
NC
HEM
1_555
A
HEM
201
B
FE
HEM
1_555
A
HEM
201
B
ND
HEM
1_555
89.7
A
HIS
39
A
NE2
HIS
37
1_555
A
HEM
201
B
FE
HEM
1_555
A
HIS
63
A
NE2
HIS
61
1_555
166.3
A
HEM
201
B
NA
HEM
1_555
A
HEM
201
B
FE
HEM
1_555
A
HIS
63
A
NE2
HIS
61
1_555
98.0
A
HEM
201
B
NB
HEM
1_555
A
HEM
201
B
FE
HEM
1_555
A
HIS
63
A
NE2
HIS
61
1_555
94.4
A
HEM
201
B
NC
HEM
1_555
A
HEM
201
B
FE
HEM
1_555
A
HIS
63
A
NE2
HIS
61
1_555
77.2
A
HEM
201
B
ND
HEM
1_555
A
HEM
201
B
FE
HEM
1_555
A
HIS
63
A
NE2
HIS
61
1_555
76.0
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
A
O
MET
23
A
O
MET
21
A
N
TYR
30
A
N
TYR
28
A
O
VAL
29
A
O
VAL
27
A
N
GLY
77
A
N
GLY
75
1
A
CA
SER
57
PLANAR
1
3.81
0.50
120.30
124.11
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
15
15
15
N
1
3.48
0.50
120.30
123.78
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
28
28
28
N
1
-5.96
0.90
118.30
112.34
A
A
A
CB
CG
OD2
ASP
ASP
ASP
31
31
31
N
1
12.80
1.90
110.10
122.90
A
A
A
CB
CA
C
SER
SER
SER
57
57
57
N
1
-5.56
0.90
118.30
112.74
A
A
A
CB
CG
OD2
ASP
ASP
ASP
60
60
60
N
1
-5.93
0.90
118.30
112.37
A
A
A
CB
CG
OD2
ASP
ASP
ASP
66
66
66
N
1
-4.00
0.60
121.00
117.00
A
A
A
CB
CG
CD2
TYR
TYR
TYR
75
75
75
N
1
8.40
0.90
118.30
126.70
A
A
A
CB
CG
OD1
ASP
ASP
ASP
83
83
83
N
1
-7.21
0.90
118.30
111.09
A
A
A
CB
CG
OD2
ASP
ASP
ASP
83
83
83
N
1
-44.51
2.10
128.40
83.89
A
A
A
C
N
CD
LYS
PRO
PRO
85
86
86
Y
1
A
A
CD
OE2
GLU
GLU
19
19
0.067
0.011
1.252
1.319
N
1
A
A
CD
OE2
GLU
GLU
20
20
0.072
0.011
1.252
1.324
N
1
A
A
CD
OE2
GLU
GLU
43
43
0.071
0.011
1.252
1.323
N
1
A
A
CD
OE2
GLU
GLU
44
44
0.096
0.011
1.252
1.348
N
1
A
A
CD
OE1
GLU
GLU
59
59
0.070
0.011
1.252
1.322
N
1
A
A
CD
OE2
GLU
GLU
69
69
0.074
0.011
1.252
1.326
N
1
A
ARG
15
-89.12
44.97
1
A
THR
33
-29.56
-59.24
1
A
LEU
36
-21.77
-51.53
1
A
HIS
39
-51.99
106.06
0.2200000
2.7
20.0
3123
3123
3123
96.
1
TNT
0.0
MOLECULAR REPLACEMENT
PDB ENTRY 3B5C
TNT
BSOL
99.7
0.79
2.7
20.0
0
719
43
0
676
0.016
744
0.8
2.9
1003
1.3
20
412
0.
0
0.007
23
2.0
0.012
104
5.
4.99
692
2.
0.023
25
10.0
36.
2.7
20.0
1B5M
3123
0.0
0.0490000
1
1.5
2.5
96.
2.7
3.05
1.0
0.0880000
4.
85.
model building
MRCHK
refinement
TNT
5E
data reduction
FRAMBO
data reduction
SADIE
data scaling
SAINT
phasing
MRCHK
RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5
1
N
N
2
N
N
A
LEU
9
A
LEU
7
HELX_P
A
LYS
14
A
LYS
12
1
1
6
A
GLU
44
A
GLU
42
HELX_P
A
GLN
49
A
GLN
47
1
2
6
A
THR
55
A
THR
53
HELX_P
A
VAL
61
A
VAL
59
1
3
7
A
PRO
65
A
PRO
63
HELX_P
A
GLN
73
A
GLN
71
1
4
9
metalc
1.918
A
HIS
39
A
NE2
HIS
37
1_555
A
HEM
201
B
FE
HEM
1_555
metalc
1.820
A
HIS
63
A
NE2
HIS
61
1_555
A
HEM
201
B
FE
HEM
1_555
ELECTRON TRANSPORT
CYTOCHROME, ELECTRON TRANSPORT, HEME
CYM5_RAT
UNP
1
1
P04166
MATPEASGSGRNGQGSDPAVTYYRLEEVAKRNTAEETWMVIHGRVYDITRFLSEHPGGEEVLLEQAGADATESFEDVGHS
PDAREMLKQYYIGDVHPNDLKPKDGDKDPSKNNSCQSSWAYWIVPIVGAILIGFLYRHFWADSKSS
19
102
1B5M
3
86
P04166
A
1
1
84
3
anti-parallel
anti-parallel
A
TRP
22
A
TRP
20
A
ILE
25
A
ILE
23
A
ARG
28
A
ARG
26
A
ASP
31
A
ASP
29
A
TYR
75
A
TYR
73
A
ASP
78
A
ASP
76
BINDING SITE FOR RESIDUE HEM A 201
A
HEM
201
Software
16
A
PHE
35
A
PHE
33
16
1_555
A
HIS
39
A
HIS
37
16
1_555
A
PRO
40
A
PRO
38
16
1_555
A
GLY
41
A
GLY
39
16
1_555
A
GLU
44
A
GLU
42
16
5_355
A
LEU
46
A
LEU
44
16
1_555
A
GLN
49
A
GLN
47
16
1_555
A
ALA
54
A
ALA
52
16
1_555
A
SER
57
A
SER
55
16
1_555
A
PHE
58
A
PHE
56
16
1_555
A
VAL
61
A
VAL
59
16
1_555
A
HIS
63
A
HIS
61
16
1_555
A
SER
64
A
SER
62
16
1_555
A
ALA
67
A
ALA
65
16
1_555
A
ARG
68
A
ARG
66
16
5_345
A
LEU
71
A
LEU
69
16
1_555
96
P 43 21 2