1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Maglio, O.
Nastri, F.
Pavone, V.
Lombardi, A.
DeGrado, W.F.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
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 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
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
H2 N
16.023
AMINO GROUP
non-polymer
C5 H9 N O2
115.130
y
PROLINE
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
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
100
3772
3777
10.1073/pnas.0730771100
12655072
Preorganization of molecular binding sites in designed diiron proteins
2003
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
97
6298
6305
10.1073/pnas.97.12.6298
Retrostructural Analysis of Metalloproteins. Application to the Design of a Minimal Model for Diiron Proteins
2000
UK
CURR.OPIN.STRUCT.BIOL.
COSBEF
0801
0959-440X
9
500
508
10.1016/S0959-440X(99)80071-2
Tertiary Templates for the Design of Diiron Protein
1999
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
123
12749
12757
10.1021/ja010506x
Toward the De Novo Design of a Catalytically Active Helix Bundle: a Substrate-Accessible Carboxylate-Bridged Dinuclear Metal Center
2001
GE
Angew.Chem.Int.Ed.Engl.
ACIEAY
0179
0570-0833
42
417
420
10.1002/anie.200390127
Sliding Helix and Change of Coordination Geometry in a Model di-Mn(II) Protein
2003
10.2210/pdb1nvo/pdb
pdb_00001nvo
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
SINGLE WAVELENGTH
M
1
1.0
5870.894
Homodimeric Alpha2 Four-Helix Bundle
2
syn
polymer
no
yes
(ACE)DYLRELLKLELQLIKQYREALEYVKLPVLAKILEDEEKHIEWLETILG(NH2)
XDYLRELLKLELQLIKQYREALEYVKLPVLAKILEDEEKHIEWLETILGX
A,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
database_2
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2003-03-25
1
1
2008-04-29
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
1EC5 is the crystal structure of DF1-di-Zn(II) derivative
1JMB is the crystal structure of a DF1 mutant (L13A-DF1) in the di-Mn(II) form (S.G. C 2 2 21)
1JM0 is a different crystalline form (S. G. P212121) of 1JMB
1LT1 is the crystal structure of L13G-DF1 in the di-Mn(II) form
RCSB
Y
RCSB
2003-02-04
REL
REL
Chemically Synthesized
sample
This structure was determined using standard 2D homonuclear techniques
structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
40
14
2D TOCSY
2D NOESY
DQF-COSY
4.0
Ambient
298
K
Torsion Angle Dynamics, Simulated Annealing, Energy Restrained Minimization
1
closest to the average
1.0 mM protein concentration; 90% H2O, 10% DMSO
90% H2O, 10% DMSO
Delaglio et al.
processing
NMRPipe
Guentert et al.
structure solution
DYANA
1.5
Case et al.
refinement
Amber
7.0
600
Bruker
AVANCE
ACE
0
n
1
ACE
0
A
ASP
1
n
2
ASP
1
A
TYR
2
n
3
TYR
2
A
LEU
3
n
4
LEU
3
A
ARG
4
n
5
ARG
4
A
GLU
5
n
6
GLU
5
A
LEU
6
n
7
LEU
6
A
LEU
7
n
8
LEU
7
A
LYS
8
n
9
LYS
8
A
LEU
9
n
10
LEU
9
A
GLU
10
n
11
GLU
10
A
LEU
11
n
12
LEU
11
A
GLN
12
n
13
GLN
12
A
LEU
13
n
14
LEU
13
A
ILE
14
n
15
ILE
14
A
LYS
15
n
16
LYS
15
A
GLN
16
n
17
GLN
16
A
TYR
17
n
18
TYR
17
A
ARG
18
n
19
ARG
18
A
GLU
19
n
20
GLU
19
A
ALA
20
n
21
ALA
20
A
LEU
21
n
22
LEU
21
A
GLU
22
n
23
GLU
22
A
TYR
23
n
24
TYR
23
A
VAL
24
n
25
VAL
24
A
LYS
25
n
26
LYS
25
A
LEU
26
n
27
LEU
26
A
PRO
27
n
28
PRO
27
A
VAL
28
n
29
VAL
28
A
LEU
29
n
30
LEU
29
A
ALA
30
n
31
ALA
30
A
LYS
31
n
32
LYS
31
A
ILE
32
n
33
ILE
32
A
LEU
33
n
34
LEU
33
A
GLU
34
n
35
GLU
34
A
ASP
35
n
36
ASP
35
A
GLU
36
n
37
GLU
36
A
GLU
37
n
38
GLU
37
A
LYS
38
n
39
LYS
38
A
HIS
39
n
40
HIS
39
A
ILE
40
n
41
ILE
40
A
GLU
41
n
42
GLU
41
A
TRP
42
n
43
TRP
42
A
LEU
43
n
44
LEU
43
A
GLU
44
n
45
GLU
44
A
THR
45
n
46
THR
45
A
ILE
46
n
47
ILE
46
A
LEU
47
n
48
LEU
47
A
GLY
48
n
49
GLY
48
A
NH2
49
n
50
NH2
49
A
ACE
0
n
1
ACE
0
B
ASP
1
n
2
ASP
1
B
TYR
2
n
3
TYR
2
B
LEU
3
n
4
LEU
3
B
ARG
4
n
5
ARG
4
B
GLU
5
n
6
GLU
5
B
LEU
6
n
7
LEU
6
B
LEU
7
n
8
LEU
7
B
LYS
8
n
9
LYS
8
B
LEU
9
n
10
LEU
9
B
GLU
10
n
11
GLU
10
B
LEU
11
n
12
LEU
11
B
GLN
12
n
13
GLN
12
B
LEU
13
n
14
LEU
13
B
ILE
14
n
15
ILE
14
B
LYS
15
n
16
LYS
15
B
GLN
16
n
17
GLN
16
B
TYR
17
n
18
TYR
17
B
ARG
18
n
19
ARG
18
B
GLU
19
n
20
GLU
19
B
ALA
20
n
21
ALA
20
B
LEU
21
n
22
LEU
21
B
GLU
22
n
23
GLU
22
B
TYR
23
n
24
TYR
23
B
VAL
24
n
25
VAL
24
B
LYS
25
n
26
LYS
25
B
LEU
26
n
27
LEU
26
B
PRO
27
n
28
PRO
27
B
VAL
28
n
29
VAL
28
B
LEU
29
n
30
LEU
29
B
ALA
30
n
31
ALA
30
B
LYS
31
n
32
LYS
31
B
ILE
32
n
33
ILE
32
B
LEU
33
n
34
LEU
33
B
GLU
34
n
35
GLU
34
B
ASP
35
n
36
ASP
35
B
GLU
36
n
37
GLU
36
B
GLU
37
n
38
GLU
37
B
LYS
38
n
39
LYS
38
B
HIS
39
n
40
HIS
39
B
ILE
40
n
41
ILE
40
B
GLU
41
n
42
GLU
41
B
TRP
42
n
43
TRP
42
B
LEU
43
n
44
LEU
43
B
GLU
44
n
45
GLU
44
B
THR
45
n
46
THR
45
B
ILE
46
n
47
ILE
46
B
LEU
47
n
48
LEU
47
B
GLY
48
n
49
GLY
48
B
NH2
49
n
50
NH2
49
B
author_defined_assembly
2
dimeric
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
TYR
2
0.088
SIDE CHAIN
1
B
TYR
2
0.072
SIDE CHAIN
1
B
TYR
17
0.087
SIDE CHAIN
2
B
TYR
2
0.105
SIDE CHAIN
3
A
TYR
2
0.182
SIDE CHAIN
3
A
TYR
17
0.085
SIDE CHAIN
3
B
TYR
2
0.066
SIDE CHAIN
4
A
TYR
2
0.083
SIDE CHAIN
4
B
TYR
2
0.071
SIDE CHAIN
4
B
TYR
17
0.085
SIDE CHAIN
5
A
TYR
17
0.071
SIDE CHAIN
6
B
TYR
2
0.079
SIDE CHAIN
7
A
TYR
17
0.128
SIDE CHAIN
8
B
TYR
2
0.087
SIDE CHAIN
9
B
TYR
2
0.090
SIDE CHAIN
10
A
TYR
2
0.068
SIDE CHAIN
10
A
TYR
23
0.078
SIDE CHAIN
11
A
TYR
17
0.094
SIDE CHAIN
12
A
TYR
17
0.144
SIDE CHAIN
12
B
TYR
2
0.135
SIDE CHAIN
13
A
TYR
2
0.105
SIDE CHAIN
13
A
TYR
17
0.069
SIDE CHAIN
13
B
ARG
4
0.087
SIDE CHAIN
13
B
TYR
17
0.073
SIDE CHAIN
14
B
TYR
17
0.065
SIDE CHAIN
1
-4.29
0.60
121.00
116.71
A
A
A
CB
CG
CD2
TYR
TYR
TYR
2
2
2
N
6
-3.62
0.60
121.00
117.38
A
A
A
CB
CG
CD2
TYR
TYR
TYR
2
2
2
N
8
-3.76
0.60
121.00
117.24
A
A
A
CB
CG
CD2
TYR
TYR
TYR
2
2
2
N
1
A
LEU
7
-131.33
-43.46
1
A
GLU
44
-75.92
27.56
1
A
THR
45
-148.30
-51.01
1
A
LEU
47
72.53
-54.14
1
B
LEU
7
-145.59
-61.79
2
A
TYR
2
-19.10
-55.35
2
A
LEU
6
-95.19
37.51
2
A
LEU
7
-144.51
-57.83
2
A
ILE
46
-26.25
-58.31
2
A
LEU
47
-170.71
134.02
2
B
TYR
2
-26.81
-69.76
2
B
LEU
7
-151.39
-66.45
2
B
GLU
44
-76.86
35.75
2
B
THR
45
-150.22
-48.27
2
B
ILE
46
36.21
66.22
3
A
LEU
7
-130.99
-51.95
3
A
ILE
46
35.67
67.55
3
A
LEU
47
57.87
16.20
3
B
GLU
5
-137.44
-50.24
4
A
GLU
5
-102.59
-63.33
4
A
LEU
6
-83.67
33.97
4
A
LEU
7
-143.66
-55.47
4
B
GLU
5
-102.28
-74.07
4
B
LEU
47
64.63
-138.47
5
A
LEU
7
-135.67
-47.78
5
A
LYS
25
61.69
63.99
5
A
THR
45
-152.71
-46.43
5
A
LEU
47
62.87
79.80
5
B
LEU
7
-133.60
-62.66
5
B
GLU
44
-75.47
27.30
5
B
THR
45
-150.16
-45.46
5
B
ILE
46
39.80
49.20
6
A
LEU
7
-160.58
-58.09
6
B
GLU
5
-127.28
-69.46
6
B
LEU
7
-140.20
-53.77
6
B
LYS
25
62.40
71.11
6
B
ILE
46
-27.28
111.03
7
A
TYR
2
-20.01
-57.58
7
A
GLU
5
-98.23
-66.13
7
B
GLU
5
-112.65
-160.77
7
B
LEU
7
-177.62
-59.59
7
B
GLU
44
-77.79
36.94
7
B
THR
45
-156.65
-49.11
7
B
ILE
46
43.69
-136.55
8
A
LEU
3
-164.12
66.61
8
A
ARG
4
-153.89
-7.65
8
A
LEU
7
-129.18
-51.95
8
B
GLU
5
-125.73
-76.88
8
B
LEU
6
-68.02
6.78
8
B
LEU
7
-127.49
-56.31
8
B
THR
45
-143.96
-46.28
9
A
LEU
7
-160.76
-52.93
9
A
PRO
27
-76.06
39.29
9
A
GLU
44
-76.58
30.51
9
A
THR
45
-154.59
-44.23
9
B
GLU
5
-120.55
-69.39
9
B
LEU
7
-122.95
-53.65
9
B
LEU
21
-96.62
-65.06
9
B
VAL
24
-88.69
-92.56
9
B
LYS
25
173.38
26.85
9
B
GLU
44
-81.93
35.36
9
B
THR
45
-148.21
-47.08
9
B
ILE
46
37.88
63.13
10
A
TYR
2
-10.46
-53.38
10
A
LEU
7
-136.00
-50.92
10
A
GLU
44
-76.99
38.93
10
A
THR
45
-162.86
-28.04
10
A
ILE
46
-55.55
98.15
10
A
LEU
47
65.68
164.27
10
B
LEU
7
-104.02
-65.73
10
B
GLU
44
-75.43
28.62
10
B
THR
45
-151.08
-49.82
11
A
TYR
2
-22.36
-49.38
11
A
LEU
3
-130.39
-30.40
11
A
LEU
7
-153.04
-70.36
11
B
TYR
2
-26.90
-67.00
11
B
LEU
7
-148.43
-62.20
11
B
GLU
44
-71.26
26.60
11
B
THR
45
-154.06
-45.09
12
A
LEU
3
-88.95
40.42
12
A
LEU
6
-69.51
2.83
12
A
GLU
44
-75.80
22.02
12
A
THR
45
-146.17
-54.15
12
A
ILE
46
57.20
157.65
12
B
GLU
5
-89.81
-71.11
12
B
GLU
44
-78.42
29.29
12
B
THR
45
-153.37
-42.29
13
A
ILE
46
-43.59
101.64
13
A
LEU
47
-166.13
-53.70
13
B
LEU
7
-135.45
-63.15
13
B
LYS
25
56.98
71.13
14
A
LEU
7
-152.27
-58.04
14
A
LEU
47
66.37
-70.08
14
B
LEU
6
-84.92
38.30
14
B
LEU
7
-153.92
-72.19
14
B
GLU
44
-74.07
25.75
14
B
THR
45
-147.90
-45.69
14
B
LEU
47
-69.39
86.04
Solution structure of a four-helix bundle model, apo-DF1
1
N
N
1
N
N
A
LEU
7
A
LEU
8
HELX_P
A
LYS
25
A
LYS
26
1
1
19
A
LEU
26
A
LEU
27
HELX_P
A
GLU
44
A
GLU
45
1
2
19
B
ASP
1
B
ASP
2
HELX_P
B
LEU
7
B
LEU
8
1
3
7
B
LEU
7
B
LEU
8
HELX_P
B
TYR
23
B
TYR
24
1
4
17
B
LEU
26
B
LEU
27
HELX_P
B
ILE
46
B
ILE
47
1
5
21
covale
1.337
both
A
ACE
0
A
C
ACE
1
1_555
A
ASP
1
A
N
ASP
2
1_555
covale
1.334
both
A
GLY
48
A
C
GLY
49
1_555
A
NH2
49
A
N
NH2
50
1_555
covale
1.336
both
B
ACE
0
B
C
ACE
1
1_555
B
ASP
1
B
N
ASP
2
1_555
covale
1.334
both
B
GLY
48
B
C
GLY
49
1_555
B
NH2
49
B
N
NH2
50
1_555
UNKNOWN FUNCTION
De Novo Protein Design, Alpha-Helical Bundle, Diiron Protein Model, UNKNOWN FUNCTION
1NVO
PDB
1
1NVO
0
49
1NVO
0
49
1NVO
A
1
1
50
0
49
1NVO
0
49
1NVO
B
1
1
50
BINDING SITE FOR RESIDUE NH2 A 49
A
NH2
49
Software
1
BINDING SITE FOR RESIDUE NH2 B 49
B
NH2
49
Software
1
A
GLY
48
A
GLY
49
1
1_555
B
GLY
48
B
GLY
49
1
1_555