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.K.
Harm, K.S.
Kim, Y.M.
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
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
To be published
0353
Interactions between antimicrobial peptide, HP(2-20) derived from helicobacter pylori, and membrain studied by nmr spectroscopy
10.2210/pdb1p0g/pdb
pdb_00001p0g
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
2325.836
19-mer peptide from 50S ribosomal protein L1
1
syn
polymer
ribosomal protein L1
no
yes
AKKVFKRLEKLFSKIQNDK(NH2)
AKKVFKRLEKLFSKIQNDKX
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
database_2
pdbx_nmr_exptl_sample_conditions
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
Experimental preparation
1
0
2003-05-20
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_exptl_sample_conditions.pressure_units
_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
HP (2-20) analogue 1
HP (2-20) analogue 2
HP (2-20) analogue 3
RCSB
Y
PDBJ
2003-04-10
REL
REL
The peptide was chemically synthesized. The sequence of peptide is naturally found in Helicobacter pylori
sample
THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES
structures with the lowest energy
50
20
2D NOESY
DQF-COSY
6
1
atm
318
K
HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING
1.5MM PEPTIDE; 150MM SDS-D25
90% H2O/10% D2O
processing
Felix
95.0
collection
XwinNMR
2.5
refinement
CNS
1.1
400
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
ASP
18
n
18
ASP
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
1
A
LYS
2
-94.77
46.20
1
A
GLN
16
-94.08
30.09
2
A
LYS
2
-93.75
47.90
2
A
ASP
18
-95.06
-65.39
3
A
LYS
2
-94.45
47.83
3
A
ASP
18
-62.28
-75.08
4
A
LYS
2
-100.10
55.03
4
A
LYS
3
-91.59
41.14
5
A
LYS
2
-99.56
48.45
6
A
LYS
2
-92.29
49.69
6
A
ASN
17
-61.64
-175.95
7
A
LYS
2
-95.20
47.09
8
A
LYS
2
-98.03
47.76
8
A
LYS
3
-160.48
39.32
9
A
LYS
2
-99.62
53.69
9
A
ASP
18
-94.87
44.73
10
A
LYS
2
-98.31
47.82
10
A
LYS
3
-151.30
38.20
11
A
LYS
2
-99.97
47.05
11
A
LYS
3
-149.71
38.03
11
A
ASP
18
-82.81
-73.92
12
A
LYS
2
-100.03
52.40
12
A
LYS
3
39.47
39.65
12
A
ASP
18
-92.86
-61.55
13
A
LYS
2
-100.05
53.59
13
A
LYS
3
-98.57
37.49
14
A
LYS
2
-96.49
47.97
15
A
LYS
2
-99.98
54.05
15
A
LYS
3
-95.46
41.18
15
A
ASP
18
-95.16
30.65
16
A
LYS
2
-96.92
46.29
16
A
LYS
3
-145.63
38.25
16
A
ASP
18
-95.21
30.92
17
A
LYS
2
-93.04
48.42
17
A
LYS
3
-100.55
40.07
17
A
GLN
16
-97.24
37.17
18
A
LYS
2
-94.25
47.75
18
A
LYS
3
-148.29
39.01
18
A
ASN
17
-95.04
35.83
19
A
LYS
2
-99.97
46.67
20
A
LYS
2
-93.52
48.12
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
GLN
16
A
GLN
16
1
1
13
covale
1.328
both
A
LYS
19
A
C
LYS
19
1_555
A
NH2
20
A
N
NH2
20
1_555
RIBOSOME
coil-helix-coil, RIBOSOME
RL1_HELPJ
UNP
1
2
Q9ZK21
AKKVFKRLEKLFSKIQNDK
2
20
1P0G
1
19
Q9ZK21
A
1
1
19
BINDING SITE FOR RESIDUE NH2 A 20
A
NH2
20
Software
1
A
LYS
19
A
LYS
19
1
1_555