1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Lee, K.H.
Lee, D.G.
Park, Y.
Hahm, K.-S.
Kim, Y.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
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
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
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
To be published
0353
Structure of Antimicrobial Peptide, HP (2-20) and its Analogues Derived from Helicobacter pylori, as Determined by 1H NMR Spectroscopy
10.2210/pdb1ot0/pdb
pdb_00001ot0
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
2396.958
50S ribosomal protein L1
N-terminal residues 2-20
1
nat
polymer
no
yes
AKKVFKRLEKLFSKIQNWK(NH2)
AKKVFKRLEKLFSKIQNWKX
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Helicobacter
sample
210
Helicobacter pylori
database_2
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2004-09-07
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_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2003-03-21
REL
structures with acceptable covalent geometry
80
20
2D TOCSY, NOESY, DQF-COSY, PECOSY
6.0
ambient
318
K
DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING
8
lowest energy
1.5MM PEPTIDE; 150MM SDS MICELLES;
90% H2O/10% D2O
BRUNGER
structure solution
CNS
1.1
data analysis
XwinNMR
2.5
processing
Felix
95.0
BRUNGER
refinement
CNS
1.1
400
Bruker
AVANCE
500
Bruker
AVANCE
ALA
1
n
1
ALA
1
A
LYS
2
n
2
LYS
2
A
LYS
3
n
3
LYS
3
A
VAL
4
n
4
VAL
4
A
PHE
5
n
5
PHE
5
A
LYS
6
n
6
LYS
6
A
ARG
7
n
7
ARG
7
A
LEU
8
n
8
LEU
8
A
GLU
9
n
9
GLU
9
A
LYS
10
n
10
LYS
10
A
LEU
11
n
11
LEU
11
A
PHE
12
n
12
PHE
12
A
SER
13
n
13
SER
13
A
LYS
14
n
14
LYS
14
A
ILE
15
n
15
ILE
15
A
GLN
16
n
16
GLN
16
A
ASN
17
n
17
ASN
17
A
TRP
18
n
18
TRP
18
A
LYS
19
n
19
LYS
19
A
NH2
20
n
20
NH2
20
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
2
A
LYS
3
-176.37
38.99
3
A
LYS
2
-98.58
33.24
3
A
LYS
3
-140.34
38.56
5
A
LYS
2
-98.67
30.58
6
A
LYS
2
-99.60
33.48
8
A
LYS
3
-172.00
38.70
9
A
LYS
2
-97.90
38.79
9
A
LYS
3
-99.06
37.84
10
A
LYS
3
-167.16
35.91
12
A
LYS
2
-98.56
30.63
13
A
LYS
2
-98.45
31.80
13
A
LYS
3
-104.35
40.77
14
A
LYS
2
-98.46
37.83
15
A
LYS
2
-98.16
36.62
17
A
LYS
2
-99.90
31.34
17
A
LYS
3
-156.00
37.25
18
A
LYS
2
-98.75
36.14
18
A
LYS
3
-99.84
38.77
19
A
LYS
2
-98.94
31.27
19
A
LYS
3
-166.10
37.91
Structure of Antimicrobial Peptide, HP (2-20) and its Analogues Derived from Helicobacter pylori, as Determined by 1H NMR Spectroscopy
1
N
N
A
VAL
4
A
VAL
4
HELX_P
A
LYS
19
A
LYS
19
1
1
16
covale
1.328
both
A
LYS
19
A
C
LYS
19
1_555
A
NH2
20
A
N
NH2
20
1_555
ANTIBIOTIC
coil-helix-coil, Ribosomal protein, rRNA-binding, Antibiotic
RL1_HELPY
UNP
1
2
P56029
AKKVFKRLEKLFSKIQNDK
2
20
1OT0
1
19
P56029
A
1
1
19
1
ASP
conflict
TRP
18
1OT0
A
P56029
UNP
19
18
BINDING SITE FOR RESIDUE NH2 A 20
A
NH2
20
Software
2
A
GLN
16
A
GLN
16
2
1_555
A
LYS
19
A
LYS
19
2
1_555