1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Morelli, X.
Guerlesquin, F.
Czjzek, M.
Palma, P.N.
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
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
Fe4 S4
351.640
IRON/SULFUR CLUSTER
non-polymer
C4 H9 N O3
119.119
y
THREONINE
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
39
2530
10.1021/BI992306S
10704202
Heteronuclear NMR and Soft Docking: An Experimental Approach for a Structural Model of the Cytochrome C553-Ferredoxin Complex
2000
US
Proteins: Struct.,Funct., Genet.
PSFGEY
0867
0887-3585
39
372
10.1002/(SICI)1097-0134(20000601)39:4<372::AID-PROT100>3.3.CO;2-H
10813819
Bigger: A New (Soft) Docking Algorithm for Predicting Protein Interactions
2000
NE
FEBS Lett.
FEBLAL
0165
0014-5793
460
77
10.1016/S0014-5793(99)01299-5
10571064
Mapping the Cytochrome C553 Interacting Site Using 1H and 15N NMR
1999
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
CONTAINS A FE4S4 CLUSTER COVALENTLY LINKED BY FOUR CYSTEINS
6264.021
FERREDOXIN I
1
man
polymer
CONTAINS A HEME GROUP COVALENTLY LINKED BY 2 CYSTEINES AND THE IRON ATOM IS COORDINATED BY A HISTIDINE AND A METHIONINE
8317.532
CYTOCHROME C553
1
nat
polymer
351.640
IRON/SULFUR CLUSTER
1
syn
non-polymer
618.503
HEME C
1
syn
non-polymer
LOW POTENTIAL CYTOCHROME C
no
no
TIVIDHEECIGCESCVELCPEVFAMIDGEEKAMVTAPDSTAECAQDAIDACPVEAISKE
TIVIDHEECIGCESCVELCPEVFAMIDGEEKAMVTAPDSTAECAQDAIDACPVEAISKE
A
polypeptide(L)
no
no
ADGAALYKSCIGCHGADGSKAAMGSAKPVKGQGAEELYKKMKGYADGSYGGERKAMMTNAVKKYSDEELKALADYMSKL
ADGAALYKSCIGCHGADGSKAAMGSAKPVKGQGAEELYKKMKGYADGSYGGERKAMMTNAVKKYSDEELKALADYMSKL
B
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
sample
PERIPLASM
FDXI
52561
DESULFOMICROBIUM NORVEGICUM
511693
ESCHERICHIA COLI
BL21
sample
CYTOPLASM
882
DESULFOVIBRIO VULGARIS
HILDENBOROUGH
repository
Initial release
Version format compliance
Version format compliance
1
0
1999-12-10
1
1
2011-05-07
1
2
2011-07-13
CYTOCHROME C553 (REDUCED) (NMR, 36 STRUCTURES)
THE Y64A MUTANT OF CYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH, NMR, 39 STRUCTURES
FERREDOXIN II OF DESULFOVIBRIO GIGAS (CRYSTAL STRUCTURE)
PDBE
Y
PDBE
1999-12-08
REL
SF4
IRON/SULFUR CLUSTER
HEC
HEME C
HETERONUCLEAR EXPERIMENTS ON 15N-LABELED FERREDOXIN AND CYTOCHROME, CHEMICAL SHIFT VARIATION ANALYSIS
COMBINATION OF NMR SHIFT VARIATION AND A SOFT DOCKING ALGORITHM
3
HSQC
5.9
pH
296
K
MOLECULAR DYNAMICS CALCULATION USING AMBER FORCE FIELD THESE ARE 3 MODEL STRUCTURES FOR THE COMPLEX OF CYTOCHROME C553 WITH FERREDOXIN I
MAPPING OF THE CHEMICAL SHIFT VARIATIONS
2
10% D2O/90% WATER
BRUNGER
refinement
X-PLOR
3.851
500
Bruker
DRX
SF4
60
3
SF4
SF4
60
A
HEC
80
4
HEC
HEC
80
B
THR
1
n
1
THR
1
A
ILE
2
n
2
ILE
2
A
VAL
3
n
3
VAL
3
A
ILE
4
n
4
ILE
4
A
ASP
5
n
5
ASP
5
A
HIS
6
n
6
HIS
6
A
GLU
7
n
7
GLU
7
A
GLU
8
n
8
GLU
8
A
CYS
9
n
9
CYS
9
A
ILE
10
n
10
ILE
10
A
GLY
11
n
11
GLY
11
A
CYS
12
n
12
CYS
12
A
GLU
13
n
13
GLU
13
A
SER
14
n
14
SER
14
A
CYS
15
n
15
CYS
15
A
VAL
16
n
16
VAL
16
A
GLU
17
n
17
GLU
17
A
LEU
18
n
18
LEU
18
A
CYS
19
n
19
CYS
19
A
PRO
20
n
20
PRO
20
A
GLU
21
n
21
GLU
21
A
VAL
22
n
22
VAL
22
A
PHE
23
n
23
PHE
23
A
ALA
24
n
24
ALA
24
A
MET
25
n
25
MET
25
A
ILE
26
n
26
ILE
26
A
ASP
27
n
27
ASP
27
A
GLY
28
n
28
GLY
28
A
GLU
29
n
29
GLU
29
A
GLU
30
n
30
GLU
30
A
LYS
31
n
31
LYS
31
A
ALA
32
n
32
ALA
32
A
MET
33
n
33
MET
33
A
VAL
34
n
34
VAL
34
A
THR
35
n
35
THR
35
A
ALA
36
n
36
ALA
36
A
PRO
37
n
37
PRO
37
A
ASP
38
n
38
ASP
38
A
SER
39
n
39
SER
39
A
THR
40
n
40
THR
40
A
ALA
41
n
41
ALA
41
A
GLU
42
n
42
GLU
42
A
CYS
43
n
43
CYS
43
A
ALA
44
n
44
ALA
44
A
GLN
45
n
45
GLN
45
A
ASP
46
n
46
ASP
46
A
ALA
47
n
47
ALA
47
A
ILE
48
n
48
ILE
48
A
ASP
49
n
49
ASP
49
A
ALA
50
n
50
ALA
50
A
CYS
51
n
51
CYS
51
A
PRO
52
n
52
PRO
52
A
VAL
53
n
53
VAL
53
A
GLU
54
n
54
GLU
54
A
ALA
55
n
55
ALA
55
A
ILE
56
n
56
ILE
56
A
SER
57
n
57
SER
57
A
LYS
58
n
58
LYS
58
A
GLU
59
n
59
GLU
59
A
ALA
1
n
1
ALA
1
B
ASP
2
n
2
ASP
2
B
GLY
3
n
3
GLY
3
B
ALA
4
n
4
ALA
4
B
ALA
5
n
5
ALA
5
B
LEU
6
n
6
LEU
6
B
TYR
7
n
7
TYR
7
B
LYS
8
n
8
LYS
8
B
SER
9
n
9
SER
9
B
CYS
10
n
10
CYS
10
B
ILE
11
n
11
ILE
11
B
GLY
12
n
12
GLY
12
B
CYS
13
n
13
CYS
13
B
HIS
14
n
14
HIS
14
B
GLY
15
n
15
GLY
15
B
ALA
16
n
16
ALA
16
B
ASP
17
n
17
ASP
17
B
GLY
18
n
18
GLY
18
B
SER
19
n
19
SER
19
B
LYS
20
n
20
LYS
20
B
ALA
21
n
21
ALA
21
B
ALA
22
n
22
ALA
22
B
MET
23
n
23
MET
23
B
GLY
24
n
24
GLY
24
B
SER
25
n
25
SER
25
B
ALA
26
n
26
ALA
26
B
LYS
27
n
27
LYS
27
B
PRO
28
n
28
PRO
28
B
VAL
29
n
29
VAL
29
B
LYS
30
n
30
LYS
30
B
GLY
31
n
31
GLY
31
B
GLN
32
n
32
GLN
32
B
GLY
33
n
33
GLY
33
B
ALA
34
n
34
ALA
34
B
GLU
35
n
35
GLU
35
B
GLU
36
n
36
GLU
36
B
LEU
37
n
37
LEU
37
B
TYR
38
n
38
TYR
38
B
LYS
39
n
39
LYS
39
B
LYS
40
n
40
LYS
40
B
MET
41
n
41
MET
41
B
LYS
42
n
42
LYS
42
B
GLY
43
n
43
GLY
43
B
TYR
44
n
44
TYR
44
B
ALA
45
n
45
ALA
45
B
ASP
46
n
46
ASP
46
B
GLY
47
n
47
GLY
47
B
SER
48
n
48
SER
48
B
TYR
49
n
49
TYR
49
B
GLY
50
n
50
GLY
50
B
GLY
51
n
51
GLY
51
B
GLU
52
n
52
GLU
52
B
ARG
53
n
53
ARG
53
B
LYS
54
n
54
LYS
54
B
ALA
55
n
55
ALA
55
B
MET
56
n
56
MET
56
B
MET
57
n
57
MET
57
B
THR
58
n
58
THR
58
B
ASN
59
n
59
ASN
59
B
ALA
60
n
60
ALA
60
B
VAL
61
n
61
VAL
61
B
LYS
62
n
62
LYS
62
B
LYS
63
n
63
LYS
63
B
TYR
64
n
64
TYR
64
B
SER
65
n
65
SER
65
B
ASP
66
n
66
ASP
66
B
GLU
67
n
67
GLU
67
B
GLU
68
n
68
GLU
68
B
LEU
69
n
69
LEU
69
B
LYS
70
n
70
LYS
70
B
ALA
71
n
71
ALA
71
B
LEU
72
n
72
LEU
72
B
ALA
73
n
73
ALA
73
B
ASP
74
n
74
ASP
74
B
TYR
75
n
75
TYR
75
B
MET
76
n
76
MET
76
B
SER
77
n
77
SER
77
B
LYS
78
n
78
LYS
78
B
LEU
79
n
79
LEU
79
B
author_defined_assembly
2
dimeric
A
CYS
9
A
SG
CYS
9
1_555
A
SF4
60
C
FE1
SF4
1_555
A
SF4
60
C
S2
SF4
1_555
106.0
A
CYS
9
A
SG
CYS
9
1_555
A
SF4
60
C
FE1
SF4
1_555
A
SF4
60
C
S3
SF4
1_555
109.9
A
SF4
60
C
S2
SF4
1_555
A
SF4
60
C
FE1
SF4
1_555
A
SF4
60
C
S3
SF4
1_555
110.5
A
CYS
9
A
SG
CYS
9
1_555
A
SF4
60
C
FE1
SF4
1_555
A
SF4
60
C
S4
SF4
1_555
112.6
A
SF4
60
C
S2
SF4
1_555
A
SF4
60
C
FE1
SF4
1_555
A
SF4
60
C
S4
SF4
1_555
109.6
A
SF4
60
C
S3
SF4
1_555
A
SF4
60
C
FE1
SF4
1_555
A
SF4
60
C
S4
SF4
1_555
108.2
A
CYS
12
A
SG
CYS
12
1_555
A
SF4
60
C
FE4
SF4
1_555
A
SF4
60
C
S1
SF4
1_555
116.8
A
CYS
12
A
SG
CYS
12
1_555
A
SF4
60
C
FE4
SF4
1_555
A
SF4
60
C
S2
SF4
1_555
109.7
A
SF4
60
C
S1
SF4
1_555
A
SF4
60
C
FE4
SF4
1_555
A
SF4
60
C
S2
SF4
1_555
106.2
A
CYS
12
A
SG
CYS
12
1_555
A
SF4
60
C
FE4
SF4
1_555
A
SF4
60
C
S3
SF4
1_555
105.1
A
SF4
60
C
S1
SF4
1_555
A
SF4
60
C
FE4
SF4
1_555
A
SF4
60
C
S3
SF4
1_555
109.3
A
SF4
60
C
S2
SF4
1_555
A
SF4
60
C
FE4
SF4
1_555
A
SF4
60
C
S3
SF4
1_555
109.5
A
CYS
15
A
SG
CYS
15
1_555
A
SF4
60
C
FE3
SF4
1_555
A
SF4
60
C
S1
SF4
1_555
112.0
A
CYS
15
A
SG
CYS
15
1_555
A
SF4
60
C
FE3
SF4
1_555
A
SF4
60
C
S2
SF4
1_555
108.7
A
SF4
60
C
S1
SF4
1_555
A
SF4
60
C
FE3
SF4
1_555
A
SF4
60
C
S2
SF4
1_555
107.4
A
CYS
15
A
SG
CYS
15
1_555
A
SF4
60
C
FE3
SF4
1_555
A
SF4
60
C
S4
SF4
1_555
110.7
A
SF4
60
C
S1
SF4
1_555
A
SF4
60
C
FE3
SF4
1_555
A
SF4
60
C
S4
SF4
1_555
108.3
A
SF4
60
C
S2
SF4
1_555
A
SF4
60
C
FE3
SF4
1_555
A
SF4
60
C
S4
SF4
1_555
109.6
A
CYS
51
A
SG
CYS
51
1_555
A
SF4
60
C
FE2
SF4
1_555
A
SF4
60
C
S1
SF4
1_555
112.9
A
CYS
51
A
SG
CYS
51
1_555
A
SF4
60
C
FE2
SF4
1_555
A
SF4
60
C
S3
SF4
1_555
109.2
A
SF4
60
C
S1
SF4
1_555
A
SF4
60
C
FE2
SF4
1_555
A
SF4
60
C
S3
SF4
1_555
109.7
A
CYS
51
A
SG
CYS
51
1_555
A
SF4
60
C
FE2
SF4
1_555
A
SF4
60
C
S4
SF4
1_555
109.8
A
SF4
60
C
S1
SF4
1_555
A
SF4
60
C
FE2
SF4
1_555
A
SF4
60
C
S4
SF4
1_555
107.6
A
SF4
60
C
S3
SF4
1_555
A
SF4
60
C
FE2
SF4
1_555
A
SF4
60
C
S4
SF4
1_555
107.5
B
HIS
14
B
NE2
HIS
14
1_555
B
HEC
80
D
FE
HEC
1_555
B
HEC
80
D
NA
HEC
1_555
86.8
B
HIS
14
B
NE2
HIS
14
1_555
B
HEC
80
D
FE
HEC
1_555
B
HEC
80
D
NB
HEC
1_555
92.5
B
HEC
80
D
NA
HEC
1_555
B
HEC
80
D
FE
HEC
1_555
B
HEC
80
D
NB
HEC
1_555
90.6
B
HIS
14
B
NE2
HIS
14
1_555
B
HEC
80
D
FE
HEC
1_555
B
HEC
80
D
NC
HEC
1_555
91.7
B
HEC
80
D
NA
HEC
1_555
B
HEC
80
D
FE
HEC
1_555
B
HEC
80
D
NC
HEC
1_555
178.4
B
HEC
80
D
NB
HEC
1_555
B
HEC
80
D
FE
HEC
1_555
B
HEC
80
D
NC
HEC
1_555
89.3
B
HIS
14
B
NE2
HIS
14
1_555
B
HEC
80
D
FE
HEC
1_555
B
HEC
80
D
ND
HEC
1_555
87.8
B
HEC
80
D
NA
HEC
1_555
B
HEC
80
D
FE
HEC
1_555
B
HEC
80
D
ND
HEC
1_555
90.5
B
HEC
80
D
NB
HEC
1_555
B
HEC
80
D
FE
HEC
1_555
B
HEC
80
D
ND
HEC
1_555
178.9
B
HEC
80
D
NC
HEC
1_555
B
HEC
80
D
FE
HEC
1_555
B
HEC
80
D
ND
HEC
1_555
89.7
B
HIS
14
B
NE2
HIS
14
1_555
B
HEC
80
D
FE
HEC
1_555
B
MET
57
B
SD
MET
57
1_555
178.4
B
HEC
80
D
NA
HEC
1_555
B
HEC
80
D
FE
HEC
1_555
B
MET
57
B
SD
MET
57
1_555
91.6
B
HEC
80
D
NB
HEC
1_555
B
HEC
80
D
FE
HEC
1_555
B
MET
57
B
SD
MET
57
1_555
87.6
B
HEC
80
D
NC
HEC
1_555
B
HEC
80
D
FE
HEC
1_555
B
MET
57
B
SD
MET
57
1_555
89.9
B
HEC
80
D
ND
HEC
1_555
B
HEC
80
D
FE
HEC
1_555
B
MET
57
B
SD
MET
57
1_555
92.1
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
N
VAL
3
A
N
VAL
3
A
O
SER
57
A
O
SER
57
A
N
ALA
24
A
N
ALA
24
A
O
MET
33
A
O
MET
33
1
A
CB
ILE
26
WRONG HAND
2
A
CB
ILE
26
WRONG HAND
3
A
CB
ILE
26
WRONG HAND
1
B
B
H
H
MET
GLY
23
24
0.99
1
A
A
C
H
SER
CYS
14
15
1.46
1
B
B
HD1
O
HIS
LYS
14
20
1.59
1
A
A
O
N
SER
CYS
14
15
1.64
1
A
A
O
N
GLY
CYS
11
12
1.76
1
B
B
CG
CG
MET
ARG
23
53
2.16
2
B
B
O
HG
LYS
SER
62
65
1.21
2
A
A
HG1
O
THR
GLU
1
59
1.55
2
B
B
O
OG
LYS
SER
62
65
1.77
3
A
A
O
HG
CYS
SER
12
14
1.20
3
B
B
O
H
GLY
LEU
3
6
1.48
3
B
B
O
N
SER
GLU
65
67
1.95
3
A
A
O
OG
CYS
SER
12
14
2.14
3
B
B
O
N
GLY
GLU
33
35
2.14
1
B
MET
76
11.62
2
B
ASP
17
-10.17
2
B
GLY
24
-30.30
3
B
GLY
24
20.42
3
B
TYR
64
-10.79
1
A
A
ILE
ASP
4
5
-148.20
1
A
A
ASP
HIS
5
6
142.91
1
A
A
GLY
CYS
11
12
51.64
1
A
A
CYS
PRO
19
20
-141.95
1
A
A
GLU
ALA
54
55
-149.22
1
B
B
LYS
ALA
20
21
142.08
1
B
B
TYR
SER
64
65
-146.69
1
B
B
SER
ASP
65
66
124.87
1
B
B
LYS
LEU
78
79
141.35
2
A
A
GLY
CYS
11
12
-78.59
2
A
A
CYS
PRO
19
20
-147.36
2
A
A
CYS
PRO
51
52
-143.11
2
B
B
CYS
ILE
10
11
-149.70
2
B
B
MET
SER
76
77
137.59
3
A
A
GLY
CYS
11
12
-129.02
3
A
A
CYS
PRO
51
52
-147.18
3
B
B
ALA
ALA
21
22
-144.85
3
B
B
GLY
SER
24
25
-149.34
3
B
B
GLN
GLY
32
33
145.34
3
B
B
TYR
SER
64
65
-134.78
3
B
B
LYS
LEU
78
79
140.74
1
B
TYR
64
0.126
SIDE CHAIN
2
B
TYR
49
0.089
SIDE CHAIN
2
B
TYR
75
0.302
SIDE CHAIN
3
B
TYR
7
0.081
SIDE CHAIN
3
B
TYR
44
0.071
SIDE CHAIN
1
A
A
C
N
GLY
CYS
11
12
1.13
1
A
A
C
N
SER
CYS
14
15
0.99
1
B
B
C
N
ASP
GLU
66
67
2.97
3
B
B
C
N
TYR
SER
64
65
1.03
1
25.29
2.20
117.20
142.49
A
A
A
CA
C
N
GLY
GLY
CYS
11
11
12
Y
1
-26.65
1.60
122.70
96.05
A
A
A
O
C
N
GLY
GLY
CYS
11
11
12
Y
1
29.89
2.50
121.70
151.59
A
A
A
C
N
CA
GLY
CYS
CYS
11
12
12
Y
1
25.71
2.20
117.20
142.91
A
A
A
CA
C
N
SER
SER
CYS
14
14
15
Y
1
-28.31
1.60
122.70
94.39
A
A
A
O
C
N
SER
SER
CYS
14
14
15
Y
1
28.06
2.50
121.70
149.76
A
A
A
C
N
CA
SER
CYS
CYS
14
15
15
Y
1
15.78
2.50
121.70
137.48
A
A
A
C
N
CA
GLY
GLU
GLU
28
29
29
Y
1
-19.18
2.70
111.00
91.82
A
A
A
N
CA
C
GLU
GLU
GLU
59
59
59
N
1
-15.65
2.00
116.20
100.55
B
B
B
CA
C
N
MET
MET
GLY
23
23
24
Y
1
19.41
1.70
123.20
142.61
B
B
B
O
C
N
MET
MET
GLY
23
23
24
Y
1
14.43
2.10
122.30
136.73
B
B
B
C
N
CA
MET
GLY
GLY
23
24
24
Y
1
-18.42
2.50
113.10
94.68
B
B
B
N
CA
C
GLY
GLY
GLY
24
24
24
N
1
-15.14
2.00
110.40
95.26
B
B
B
CB
CA
C
ASP
ASP
ASP
66
66
66
N
1
-14.50
2.20
117.20
102.70
B
B
B
CA
C
N
TYR
TYR
MET
75
75
76
Y
1
20.64
1.60
122.70
143.34
B
B
B
O
C
N
TYR
TYR
MET
75
75
76
Y
1
-17.22
2.70
111.00
93.78
B
B
B
N
CA
C
LEU
LEU
LEU
79
79
79
N
2
-10.85
1.80
114.00
103.15
A
A
A
CA
CB
SG
CYS
CYS
CYS
9
9
9
N
2
-13.53
1.60
122.70
109.17
A
A
A
O
C
N
GLU
GLU
GLU
29
29
30
Y
2
-11.60
1.80
114.00
102.40
A
A
A
CA
CB
SG
CYS
CYS
CYS
51
51
51
N
2
-17.85
2.70
111.00
93.15
A
A
A
N
CA
C
GLU
GLU
GLU
59
59
59
N
2
-13.37
2.10
122.30
108.93
B
B
B
C
N
CA
HIS
GLY
GLY
14
15
15
Y
2
-15.98
2.20
117.20
101.22
B
B
B
CA
C
N
ALA
ALA
ALA
21
21
22
Y
2
16.08
1.60
122.70
138.78
B
B
B
O
C
N
ALA
ALA
ALA
21
21
22
Y
2
-28.84
2.50
121.70
92.86
B
B
B
C
N
CA
ALA
ALA
ALA
21
22
22
Y
2
11.39
1.60
122.70
134.09
B
B
B
O
C
N
ALA
ALA
MET
22
22
23
Y
2
-17.76
2.20
117.20
99.44
B
B
B
CA
C
N
GLY
GLY
SER
24
24
25
Y
2
-20.64
1.60
122.70
102.06
B
B
B
O
C
N
GLY
GLY
SER
24
24
25
Y
2
28.65
2.50
121.70
150.35
B
B
B
C
N
CA
GLY
SER
SER
24
25
25
Y
2
-21.33
2.20
117.20
95.87
B
B
B
CA
C
N
SER
SER
ASP
65
65
66
Y
2
26.54
1.60
122.70
149.24
B
B
B
O
C
N
SER
SER
ASP
65
65
66
Y
2
16.29
2.50
121.70
137.99
B
B
B
C
N
CA
SER
ASP
ASP
65
66
66
Y
2
-4.70
0.60
121.00
116.30
B
B
B
CB
CG
CD2
TYR
TYR
TYR
75
75
75
N
2
-14.89
2.20
117.20
102.31
B
B
B
CA
C
N
LYS
LYS
LEU
78
78
79
Y
2
12.94
1.60
122.70
135.64
B
B
B
O
C
N
LYS
LYS
LEU
78
78
79
Y
2
-17.16
2.70
111.00
93.84
B
B
B
N
CA
C
LEU
LEU
LEU
79
79
79
N
3
-9.18
1.50
110.50
101.32
A
A
A
N
CA
CB
SER
SER
SER
39
39
39
N
3
-18.62
2.70
111.00
92.38
A
A
A
N
CA
C
GLU
GLU
GLU
59
59
59
N
3
-13.17
1.60
122.70
109.53
B
B
B
O
C
N
ALA
ALA
ALA
4
4
5
Y
3
14.05
1.60
122.70
136.75
B
B
B
O
C
N
GLU
GLU
GLU
67
67
68
Y
3
-18.84
2.70
111.00
92.16
B
B
B
N
CA
C
LEU
LEU
LEU
79
79
79
N
1
A
A
C
N
GLY
CYS
11
12
-0.208
0.023
1.336
1.128
Y
1
A
A
C
N
SER
CYS
14
15
-0.351
0.023
1.336
0.985
Y
1
B
B
N
CA
GLU
GLU
67
67
0.130
0.020
1.459
1.589
N
1
B
B
C
N
TYR
MET
75
76
0.184
0.023
1.336
1.520
Y
2
B
B
C
N
ALA
ALA
21
22
0.187
0.023
1.336
1.523
Y
2
B
B
C
N
GLY
SER
24
25
0.201
0.023
1.336
1.537
Y
2
B
B
C
O
SER
SER
65
65
0.127
0.019
1.229
1.356
N
2
B
B
C
N
SER
ASP
65
66
0.184
0.023
1.336
1.520
Y
2
B
B
C
N
LYS
LEU
78
79
0.247
0.023
1.336
1.583
Y
3
A
A
N
CA
SER
SER
14
14
0.120
0.020
1.459
1.579
N
3
B
B
C
N
GLY
SER
24
25
0.234
0.023
1.336
1.570
Y
3
B
B
C
N
TYR
SER
64
65
-0.309
0.023
1.336
1.027
Y
3
B
B
C
N
ASP
GLU
66
67
0.154
0.023
1.336
1.490
Y
1
A
ILE
10
-144.34
56.94
1
A
GLU
13
70.69
-4.27
1
A
SER
14
-51.78
-78.99
1
A
GLU
29
47.03
5.14
1
A
GLU
30
-147.09
-15.64
1
A
SER
39
-69.62
98.57
1
A
THR
40
-65.55
66.63
1
A
ALA
50
-151.75
20.78
1
B
ASP
2
171.33
-55.33
1
B
HIS
14
-141.52
-31.15
1
B
ASP
17
-153.75
52.61
1
B
MET
23
-136.30
-38.15
1
B
LYS
54
31.70
3.39
1
B
TYR
64
-106.51
67.33
1
B
SER
65
-57.16
77.44
1
B
ASP
74
-69.66
86.75
1
B
TYR
75
-161.83
-53.29
1
B
MET
76
-67.31
79.90
1
B
SER
77
-146.39
40.63
2
A
GLU
8
-163.99
36.59
2
A
CYS
9
-101.88
66.77
2
A
GLU
13
36.65
-17.50
2
A
SER
14
-45.49
-82.32
2
A
VAL
22
-136.28
-53.09
2
A
GLU
29
54.39
-3.30
2
A
ASP
38
-129.88
-53.36
2
B
ALA
16
33.59
-2.87
2
B
ASP
17
-168.68
-1.61
2
B
SER
19
-94.87
42.97
2
B
MET
23
27.91
31.34
2
B
SER
25
37.37
61.29
2
B
LYS
30
-159.57
47.58
2
B
ARG
53
-97.29
44.09
2
B
SER
65
-40.87
93.22
2
B
ASP
66
41.43
7.53
2
B
ALA
71
-138.42
-53.74
2
B
ASP
74
-155.72
-54.53
2
B
LYS
78
-138.01
-56.37
3
A
GLU
13
17.82
-61.64
3
A
SER
14
18.19
-84.29
3
A
VAL
22
-135.94
-58.69
3
A
GLU
29
54.14
15.28
3
A
GLU
30
-167.63
-3.93
3
A
SER
39
-65.39
82.31
3
A
THR
40
-66.01
77.19
3
B
ALA
4
11.63
-92.27
3
B
LEU
6
-85.98
44.44
3
B
LYS
8
12.15
-83.62
3
B
ASP
17
-156.42
86.12
3
B
ALA
22
-90.05
41.12
3
B
SER
25
67.02
-165.08
3
B
ALA
26
166.88
-178.81
3
B
PRO
28
-58.80
108.56
3
B
GLN
32
-84.68
40.02
3
B
ALA
34
34.59
-27.19
3
B
ARG
53
-91.61
54.65
3
B
TYR
64
-113.98
67.41
3
B
ASP
66
38.73
-22.13
3
B
GLU
67
-169.45
71.65
3
B
GLU
68
-147.85
-35.70
3
B
ALA
71
-113.99
51.28
3
B
TYR
75
-171.99
-50.43
3
B
LYS
78
-161.40
-39.36
FERREDOXIN I, CYTOCHROME C553
MODELLING EXPERIMENT: THE COMPLEX STRUCTURE WAS OBTAINED BY SOFT DOCKING ALGORITHM IMPLEMENTED WITH AN NMR FILTER. THE STARTING MODELS OF THE CYTOCHROME AND THE FERREDOXIN WERE BASED ON THE PDB ENTRIES 1DVH AND 1FXD
The Ferredoxin-Cytochrome complex using heteronuclear NMR and docking simulation
1
N
N
2
N
N
3
N
N
4
N
N
A
GLU
13
A
GLU
13
HELX_P
A
LEU
18
A
LEU
18
5
1
6
A
ALA
41
A
ALA
41
HELX_P
A
ASP
46
A
ASP
46
5
2
6
A
ASP
46
A
ASP
46
HELX_P
A
CYS
51
A
CYS
51
5
3
6
B
ASP
2
B
ASP
2
HELX_P
B
TYR
7
B
TYR
7
5
4
6
B
CYS
10
B
CYS
10
HELX_P
B
GLY
15
B
GLY
15
1
5
6
B
GLY
33
B
GLY
33
HELX_P
B
ASP
46
B
ASP
46
1
6
14
B
LYS
54
B
LYS
54
HELX_P
B
TYR
64
B
TYR
64
1
7
11
B
GLU
67
B
GLU
67
HELX_P
B
ALA
73
B
ALA
73
1
8
7
metalc
2.323
A
SF4
60
C
FE1
SF4
1_555
A
CYS
9
A
SG
CYS
9
1_555
metalc
2.280
A
SF4
60
C
FE4
SF4
1_555
A
CYS
12
A
SG
CYS
12
1_555
metalc
2.336
A
SF4
60
C
FE3
SF4
1_555
A
CYS
15
A
SG
CYS
15
1_555
metalc
2.337
A
SF4
60
C
FE2
SF4
1_555
A
CYS
51
A
SG
CYS
51
1_555
covale
1.834
B
CYS
10
B
SG
CYS
10
1_555
B
HEC
80
D
CAB
HEC
1_555
covale
1.828
B
CYS
13
B
SG
CYS
13
1_555
B
HEC
80
D
CAC
HEC
1_555
metalc
2.171
B
HEC
80
D
FE
HEC
1_555
B
HIS
14
B
NE2
HIS
14
1_555
metalc
2.335
B
HEC
80
D
FE
HEC
1_555
B
MET
57
B
SD
MET
57
1_555
ELECTRON TRANSFER
ELECTRON TRANSFER, FERREDOXIN-CYTOCHROME COMPLEX, MODEL, HETERONUCLEAR NMR, DOCKING
FER1_DESDN
UNP
1
P07485
C553_DESVH
UNP
2
P04032
1
59
1DWL
1
59
P07485
A
1
1
59
25
103
1DWL
1
79
P04032
B
2
1
79
2
2
anti-parallel
anti-parallel
A
ILE
2
A
ILE
2
A
ILE
4
A
ILE
4
A
ILE
56
A
ILE
56
A
LYS
58
A
LYS
58
A
PHE
23
A
PHE
23
A
ASP
27
A
ASP
27
A
ALA
32
A
ALA
32
A
VAL
34
A
VAL
34
BINDING SITE FOR RESIDUE SF4 A 60
Software
12
BINDING SITE FOR RESIDUE HEC B 80
Software
24
A
ILE
4
A
ILE
4
12
1_555
A
CYS
9
A
CYS
9
12
1_555
A
GLY
11
A
GLY
11
12
1_555
A
CYS
12
A
CYS
12
12
1_555
A
GLU
13
A
GLU
13
12
1_555
A
SER
14
A
SER
14
12
1_555
A
CYS
15
A
CYS
15
12
1_555
A
ASP
27
A
ASP
27
12
1_555
A
ALA
47
A
ALA
47
12
1_555
A
ALA
50
A
ALA
50
12
1_555
A
CYS
51
A
CYS
51
12
1_555
A
PRO
52
A
PRO
52
12
1_555
A
CYS
12
A
CYS
12
24
1_555
A
SER
14
A
SER
14
24
1_555
B
TYR
7
B
TYR
7
24
1_555
B
CYS
10
B
CYS
10
24
1_555
B
CYS
13
B
CYS
13
24
1_555
B
HIS
14
B
HIS
14
24
1_555
B
MET
23
B
MET
23
24
1_555
B
ALA
26
B
ALA
26
24
1_555
B
LYS
27
B
LYS
27
24
1_555
B
VAL
29
B
VAL
29
24
1_555
B
LEU
37
B
LEU
37
24
1_555
B
LYS
40
B
LYS
40
24
1_555
B
MET
41
B
MET
41
24
1_555
B
TYR
44
B
TYR
44
24
1_555
B
TYR
49
B
TYR
49
24
1_555
B
GLY
51
B
GLY
51
24
1_555
B
GLU
52
B
GLU
52
24
1_555
B
ARG
53
B
ARG
53
24
1_555
B
LYS
54
B
LYS
54
24
1_555
B
MET
56
B
MET
56
24
1_555
B
MET
57
B
MET
57
24
1_555
B
TYR
64
B
TYR
64
24
1_555
B
LEU
72
B
LEU
72
24
1_555
B
MET
76
B
MET
76
24
1_555
1
P 1