1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Cochran, A.G.
Skelton, N.J.
Starovasnik, M.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C4 H8 N2 O3
132.118
y
ASPARAGINE
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 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
H2 N
16.023
AMINO GROUP
non-polymer
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
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
98
5578
5583
10.1073/pnas.091100898
11331745
Tryptophan zippers: stable, monomeric beta -hairpins.
2001
To be Published
0353
Chemical-shift-based methods for structure validation and refinement: Application to tryptophan zipper beta-hairpin peptides
10.2210/pdb1le1/pdb
pdb_00001le1
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
1608.776
Tryptophan Zipper 2
1
syn
polymer
no
yes
SWTWENGKWTWK(NH2)
SWTWENGKWTWKX
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
database_2
pdbx_nmr_software
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
2002-04-24
1
1
2008-04-28
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
2002-04-24
SPRSDE
1LE0 contains Tryptophan Zipper 1
1LE3 contains Tryptophan Zipper 4
RCSB
Y
PDBJ
2002-04-09
REL
This sequence was designed based on experimental data obtained from a model system. The peptide was chemically synthesized and does not appear to occur in nature.
sample
The structure of trpzip2 was originally determined using standard 2D homonuclear techniques (Cochran et al., 2001, Proc. Natl. Acad. Sci. USA, 98, 5578-5583). Distance and dihedral angle restraints were derived from analysis of NOESY, ROESY, DQF-COSY, and COSY-35 data. Chi-1 rotamers and stereospecific assignments for beta-methylene groups were based on combined analysis of 3JHaHb and local ROEs, suggesting that all four Trp residues adopt a chi1 of -60 deg. Quantitative analysis of the 1H chemical shifts, however, revealed that the frequencies of the Hb and He3 resonances of Trp4 and Trp11 were inconsistent with a -60 deg chi1 value, and indicated that the side chains for these tryptophans actually reside primarily in the 180 deg chi1 rotamer (Skelton et al., manuscript in preparation). The current coordinates result from refinement with the Sander module of AMBER (v6.0), and included not only NOE-derived distance restraints and dihedral angle restraints, but also 1H chemical shift-based restraints. Thus, the resulting updated coordinates differ from the previous ones in the side chain orientations of Trp4 and Trp11. However, the rest of the structure is similar with a backbone rmsd between the average coordinates of the two ensembles of 0.69 angstrom(res.2-11). The two strands are highly twisted, as described previously, however there is a slight difference in the relative position of the turn with respect to the strands. The key difference, however, is that each pair of cross-strand tryptophan rings now shows edge-to-face packing against one another.
structures with the least restraint violations
76
20
2D NOESY
DQF-COSY
2D TOCSY
2D ROESY
2D COSY-35
0
5.5
ambient
288
K
Structures are based on a total of 80 (including 26 intra-residue, 15 sequential, 6 medium-range, and 33 long-range) NOE-derived distance restraints, 15 dihedral angle restraints, and 1H chemical shift restraints for 39 carbon-bound 1H resonances; (chemical shift restraints were not imposed for the terminal residues, or for side chains exhibiting evidence of rotational averaging). The ensemble agrees well with the experimental restraints with no distance or dihedral angle violations greater than 0.10 angstrom or 5 deg, respectively, and an average rmsd of only 0.087 ppm between observed and calculated chemical shifts.
Hybrid distance geometry/simulated annealing using the program DGII, followed by molecular dynamics using the program AMBER, in conjunction not only with distance and dihedral angle restraints, but also 1H chemical shift-based restraints.
1
closest to the average
3mM trpzip2
92% H2O, 8% D2O, pH 5.5, 0.1mM DSS
Bruker
collection
XwinNMR
2.5
Molecular Simulations, Inc.
data analysis
Felix
98.0
Molecular Simulations, Inc.
structure solution
DGII
98.0
Case and Kollman
refinement
Amber
6.0
500
Bruker
DRX
SER
1
n
1
SER
1
A
TRP
2
n
2
TRP
2
A
THR
3
n
3
THR
3
A
TRP
4
n
4
TRP
4
A
GLU
5
n
5
GLU
5
A
ASN
6
n
6
ASN
6
A
GLY
7
n
7
GLY
7
A
LYS
8
n
8
LYS
8
A
TRP
9
n
9
TRP
9
A
THR
10
n
10
THR
10
A
TRP
11
n
11
TRP
11
A
LYS
12
n
12
LYS
12
A
NH2
13
n
13
NH2
13
A
author_defined_assembly
1
monomeric
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
THR
3
A
N
THR
3
A
O
THR
10
A
O
THR
10
8
A
A
HG
O
SER
LYS
1
12
1.52
14
A
A
HG
O
SER
LYS
1
12
1.54
1
A
ASN
6
31.17
71.16
2
A
ASN
6
29.80
62.76
4
A
ASN
6
50.22
18.78
6
A
ASN
6
41.60
28.30
8
A
ASN
6
33.33
44.79
9
A
ASN
6
34.84
68.84
10
A
ASN
6
34.40
51.77
11
A
ASN
6
38.01
55.10
12
A
ASN
6
45.94
24.55
13
A
ASN
6
38.37
71.61
14
A
ASN
6
27.47
72.00
15
A
ASN
6
45.07
20.80
16
A
ASN
6
29.31
61.79
17
A
TRP
2
-57.39
106.81
17
A
ASN
6
31.54
65.53
19
A
ASN
6
29.23
72.24
20
A
ASN
6
29.15
65.91
NMR Structure of Tryptophan Zipper 2: A stable, Monomeric Beta-Hairpin with a Type I' Turn
1
Y
N
covale
1.324
both
A
LYS
12
A
C
LYS
12
1_555
A
NH2
13
A
N
NH2
13
1_555
DE NOVO PROTEIN
beta-hairpin, type I' turn, DE NOVO PROTEIN
1LE1
PDB
1
1LE1
1
13
1LE1
1
13
1LE1
A
1
1
13
2
anti-parallel
A
TRP
2
A
TRP
2
A
GLU
5
A
GLU
5
A
LYS
8
A
LYS
8
A
TRP
11
A
TRP
11
BINDING SITE FOR RESIDUE NH2 A 13
A
NH2
13
Software
1
A
LYS
12
A
LYS
12
1
1_555